From a31acc32c03545b884cd9d71b38d308cb4423f33 Mon Sep 17 00:00:00 2001 From: Mark Schroering Date: Tue, 28 May 2019 13:35:24 -0400 Subject: [PATCH 1/2] Added recursive support to the files download command --- foo/out/stderr.txt | 0 foo/out/stdout.txt | 1 + .../execution-log.txt | 42 +++++ .../executor.0.stdout.txt | 1 + .../execution-log.txt | 98 ++++++++++++ .../executor.0.stderr.txt | 6 + .../executor.1.stderr.txt | 71 +++++++++ .../executor.1.stdout.txt | 7 + .../execution-log.txt | 42 +++++ .../executor.0.stdout.txt | 1 + .../execution-log.txt | 42 +++++ .../executor.0.stdout.txt | 1 + .../execution-log.txt | 150 ++++++++++++++++++ .../executor.0.stderr.txt | 6 + .../executor.1.stderr.txt | 71 +++++++++ .../executor.1.stdout.txt | 7 + .../executor.2.stderr.txt | 3 + lib/cmds/files_cmds/download.js | 44 ++++- test/unit/commands/file.test.js | 29 ++++ 19 files changed, 615 insertions(+), 7 deletions(-) create mode 100644 foo/out/stderr.txt create mode 100644 foo/out/stdout.txt create mode 100644 foo/tasks/06f054f0-c1cf-4326-91bd-758adfb049e8/execution-log.txt create mode 100644 foo/tasks/06f054f0-c1cf-4326-91bd-758adfb049e8/executor.0.stdout.txt create mode 100644 foo/tasks/1475a045-fe75-44d1-831e-bedd86403661/execution-log.txt create mode 100644 foo/tasks/1475a045-fe75-44d1-831e-bedd86403661/executor.0.stderr.txt create mode 100644 foo/tasks/1475a045-fe75-44d1-831e-bedd86403661/executor.1.stderr.txt create mode 100644 foo/tasks/1475a045-fe75-44d1-831e-bedd86403661/executor.1.stdout.txt create mode 100644 foo/tasks/58c847d7-c0ab-4d82-bfe7-86ece7a5e91a/execution-log.txt create mode 100644 foo/tasks/58c847d7-c0ab-4d82-bfe7-86ece7a5e91a/executor.0.stdout.txt create mode 100644 foo/tasks/60d1af38-8a2b-4161-9521-5090a7ce4cc7/execution-log.txt create mode 100644 foo/tasks/60d1af38-8a2b-4161-9521-5090a7ce4cc7/executor.0.stdout.txt create mode 100644 foo/tasks/66c9e1b0-866c-4c36-88a7-05e7c96780dd/execution-log.txt create mode 100644 foo/tasks/66c9e1b0-866c-4c36-88a7-05e7c96780dd/executor.0.stderr.txt create mode 100644 foo/tasks/66c9e1b0-866c-4c36-88a7-05e7c96780dd/executor.1.stderr.txt create mode 100644 foo/tasks/66c9e1b0-866c-4c36-88a7-05e7c96780dd/executor.1.stdout.txt create mode 100644 foo/tasks/66c9e1b0-866c-4c36-88a7-05e7c96780dd/executor.2.stderr.txt diff --git a/foo/out/stderr.txt b/foo/out/stderr.txt new file mode 100644 index 0000000..e69de29 diff --git a/foo/out/stdout.txt b/foo/out/stdout.txt new file mode 100644 index 0000000..3b18e51 --- /dev/null +++ b/foo/out/stdout.txt @@ -0,0 +1 @@ +hello world diff --git a/foo/tasks/06f054f0-c1cf-4326-91bd-758adfb049e8/execution-log.txt b/foo/tasks/06f054f0-c1cf-4326-91bd-758adfb049e8/execution-log.txt new file mode 100644 index 0000000..931bf07 --- /dev/null +++ b/foo/tasks/06f054f0-c1cf-4326-91bd-758adfb049e8/execution-log.txt @@ -0,0 +1,42 @@ +[2019-05-11T20:17:21.889Z] INFO: task-service-container/7 on ip-10-51-76-102: Task running on arn:aws:ecs:us-east-1:623119755067:container-instance/ab93d217-6d28-4eb9-b0bc-40b3bf705533 in cluster arn:aws:ecs:us-east-1:623119755067:cluster/task-service-v3-7k23nbyl7o1kf1f6_Batch_183d8bc1-e24f-3bc8-ad3e-b48b4ccfe131 +[2019-05-11T20:17:21.925Z] INFO: task-service-container/7 on ip-10-51-76-102: Container instance has 2048 vCPU and 7945 MB +[2019-05-11T20:17:21.926Z] INFO: task-service-container/7 on ip-10-51-76-102: Task usage (cpuUsage=0.5, memUsage=0.12586532410320955, usageFactor=0.31293266205160475) +[2019-05-11T20:17:21.927Z] INFO: task-service-container/7 on ip-10-51-76-102: dd if=/dev/zero of=/tmp/6fd84f00-c740-45a7-8813-b4bb1c62d56a-fs/disk-quota.ext3 count=1189144 +[2019-05-11T20:17:25.628Z] INFO: task-service-container/7 on ip-10-51-76-102: mkfs.ext3 /tmp/6fd84f00-c740-45a7-8813-b4bb1c62d56a-fs/disk-quota.ext3 +[2019-05-11T20:17:45.667Z] INFO: task-service-container/7 on ip-10-51-76-102: mount /tmp/6fd84f00-c740-45a7-8813-b4bb1c62d56a-fs/disk-quota.ext3 /tmp/6fd84f00-c740-45a7-8813-b4bb1c62d56a +[2019-05-11T20:17:45.731Z] INFO: task-service-container/7 on ip-10-51-76-102: Creating output directory /tmp/6fd84f00-c740-45a7-8813-b4bb1c62d56a/out (account=lifeomic, id=06f054f0-c1cf-4326-91bd-758adfb049e8) +[2019-05-11T20:17:45.732Z] INFO: task-service-container/7 on ip-10-51-76-102: Task has 86400 seconds to complete +[2019-05-11T20:18:01.060Z] INFO: task-service-container/7 on ip-10-51-76-102: Image busybox already exists, skipping pull (account=lifeomic, id=06f054f0-c1cf-4326-91bd-758adfb049e8) +[2019-05-11T20:18:01.061Z] INFO: task-service-container/7 on ip-10-51-76-102: Creating container for image busybox (account=lifeomic, id=06f054f0-c1cf-4326-91bd-758adfb049e8, Image=busybox, AttachStdin=false, AttachStdout=true, AttachStderr=true, Tty=false, OpenStdin=false, StdinOnce=false, NetworkDisabled=true, WorkingDir=/tmp) + Env: [ + "LO_USER=Google_112277633572082602793", + "LO_ACCOUNT=lifeomic", + "LO_PROJECT=db3e09e9-1ecd-4976-aa5e-70ac7ada0cc3" + ] + -- + Cmd: [ + "echo", + "hello world" + ] + -- + HostConfig: { + "Binds": [ + "/tmp/6fd84f00-c740-45a7-8813-b4bb1c62d56a/out:/out" + ], + "Ulimits": [ + { + "Name": "nofile", + "Soft": 1024000, + "Hard": 1024000 + } + ], + "StorageOpt": { + "size": "28164M" + } + } +[2019-05-11T20:18:02.101Z] INFO: task-service-container/7 on ip-10-51-76-102: Running container for image busybox (account=lifeomic, id=06f054f0-c1cf-4326-91bd-758adfb049e8) +[2019-05-11T20:18:02.593Z] INFO: task-service-container/7 on ip-10-51-76-102: Container for image busybox finished with code 0 (account=lifeomic, id=06f054f0-c1cf-4326-91bd-758adfb049e8) +[2019-05-11T20:18:02.594Z] INFO: task-service-container/7 on ip-10-51-76-102: 86383.138 seconds left for task execution (account=lifeomic, id=06f054f0-c1cf-4326-91bd-758adfb049e8) +[2019-05-11T20:18:02.594Z] INFO: task-service-container/7 on ip-10-51-76-102: Uploading executor log /tmp/6fd84f00-c740-45a7-8813-b4bb1c62d56a/out/stdout.txt (account=lifeomic, id=06f054f0-c1cf-4326-91bd-758adfb049e8) +[2019-05-11T20:18:02.888Z] INFO: task-service-container/7 on ip-10-51-76-102: Uploading output /tmp/6fd84f00-c740-45a7-8813-b4bb1c62d56a/out (account=lifeomic, id=06f054f0-c1cf-4326-91bd-758adfb049e8) +[2019-05-11T20:18:03.385Z] INFO: task-service-container/7 on ip-10-51-76-102: Uploading execution log /tmp/task-service-container.489ce091-2714-4cb3-a11a-c15593096405.log (account=lifeomic, id=06f054f0-c1cf-4326-91bd-758adfb049e8) diff --git a/foo/tasks/06f054f0-c1cf-4326-91bd-758adfb049e8/executor.0.stdout.txt b/foo/tasks/06f054f0-c1cf-4326-91bd-758adfb049e8/executor.0.stdout.txt new file mode 100644 index 0000000..3b18e51 --- /dev/null +++ b/foo/tasks/06f054f0-c1cf-4326-91bd-758adfb049e8/executor.0.stdout.txt @@ -0,0 +1 @@ +hello world diff --git a/foo/tasks/1475a045-fe75-44d1-831e-bedd86403661/execution-log.txt b/foo/tasks/1475a045-fe75-44d1-831e-bedd86403661/execution-log.txt new file mode 100644 index 0000000..d371511 --- /dev/null +++ b/foo/tasks/1475a045-fe75-44d1-831e-bedd86403661/execution-log.txt @@ -0,0 +1,98 @@ +[2019-02-20T19:17:28.970Z] INFO: task-service-container/6 on ip-10-51-66-225: Downloading input /tmp/6d161a9d-3eba-4697-bae3-8baa85403890/tmp/reference (account=lifeomic, id=1475a045-fe75-44d1-831e-bedd86403661) +[2019-02-20T19:17:46.940Z] INFO: task-service-container/6 on ip-10-51-66-225: Downloaded /tmp/6d161a9d-3eba-4697-bae3-8baa85403890/tmp/reference/GRCh37.fa.gz +[2019-02-20T19:17:47.077Z] INFO: task-service-container/6 on ip-10-51-66-225: Downloaded /tmp/6d161a9d-3eba-4697-bae3-8baa85403890/tmp/reference/GRCh37.fa.gz.fai +[2019-02-20T19:17:47.242Z] INFO: task-service-container/6 on ip-10-51-66-225: Downloaded /tmp/6d161a9d-3eba-4697-bae3-8baa85403890/tmp/reference/GRCh37.fa.gz.gzi +[2019-02-20T19:17:47.378Z] INFO: task-service-container/6 on ip-10-51-66-225: Downloaded /tmp/6d161a9d-3eba-4697-bae3-8baa85403890/tmp/reference/upload.json +[2019-02-20T19:17:47.454Z] INFO: task-service-container/6 on ip-10-51-66-225: Downloaded /tmp/6d161a9d-3eba-4697-bae3-8baa85403890/tmp/reference/version.txt +[2019-02-20T19:17:47.454Z] INFO: task-service-container/6 on ip-10-51-66-225: Downloading input /tmp/6d161a9d-3eba-4697-bae3-8baa85403890/tmp/SMP60684.xml (account=lifeomic, id=1475a045-fe75-44d1-831e-bedd86403661) +[2019-02-20T19:17:47.649Z] INFO: task-service-container/6 on ip-10-51-66-225: Creating output directory /tmp/6d161a9d-3eba-4697-bae3-8baa85403890/tmp (account=lifeomic, id=1475a045-fe75-44d1-831e-bedd86403661) +[2019-02-20T19:17:47.649Z] INFO: task-service-container/6 on ip-10-51-66-225: Creating output directory /tmp/6d161a9d-3eba-4697-bae3-8baa85403890/tmp (account=lifeomic, id=1475a045-fe75-44d1-831e-bedd86403661) +[2019-02-20T19:17:47.649Z] INFO: task-service-container/6 on ip-10-51-66-225: Creating output directory /tmp/6d161a9d-3eba-4697-bae3-8baa85403890/tmp (account=lifeomic, id=1475a045-fe75-44d1-831e-bedd86403661) +[2019-02-20T19:17:47.649Z] INFO: task-service-container/6 on ip-10-51-66-225: Creating output directory /tmp/6d161a9d-3eba-4697-bae3-8baa85403890/tmp (account=lifeomic, id=1475a045-fe75-44d1-831e-bedd86403661) +[2019-02-20T19:17:47.654Z] INFO: task-service-container/6 on ip-10-51-66-225: Pulling image lifeomic/foundation-xml-fhir (account=lifeomic, id=1475a045-fe75-44d1-831e-bedd86403661) +[2019-02-20T19:18:20.437Z] INFO: task-service-container/6 on ip-10-51-66-225: Creating container for image lifeomic/foundation-xml-fhir (account=lifeomic, id=1475a045-fe75-44d1-831e-bedd86403661, Image=lifeomic/foundation-xml-fhir, AttachStdin=false, AttachStdout=true, AttachStderr=true, Tty=false, OpenStdin=false, StdinOnce=false, NetworkDisabled=true, WorkingDir=/tmp) + Cmd: [ + "-x", + "/tmp/SMP60684.xml", + "-o", + "/tmp/output.json", + "-p", + "db3e09e9-1ecd-4976-aa5e-70ac7ada0cc3", + "-r", + "/tmp/reference/GRCh37.fa.gz", + "-s", + "45fdb72e-2059-45aa-8e61-d31ad9156058", + "-f", + "https://api.dev.lifeomic.com/v1/files/2d1ac137-91ea-4246-81f9-3e9e08ad5d1f", + "-d", + "/tmp/report.pdf", + "-v", + "/tmp/foundation.vcf" + ] + -- + HostConfig: { + "Binds": [ + "/tmp/6d161a9d-3eba-4697-bae3-8baa85403890/tmp/reference:/tmp/reference", + "/tmp/6d161a9d-3eba-4697-bae3-8baa85403890/tmp:/tmp" + ], + "Ulimits": [ + { + "Name": "nofile", + "Soft": 1024000, + "Hard": 1024000 + } + ] + } +[2019-02-20T19:18:20.984Z] INFO: task-service-container/6 on ip-10-51-66-225: Running container for image lifeomic/foundation-xml-fhir (account=lifeomic, id=1475a045-fe75-44d1-831e-bedd86403661) +[2019-02-20T19:23:48.715Z] INFO: task-service-container/6 on ip-10-51-66-225: Container for image lifeomic/foundation-xml-fhir finished with code 0 (account=lifeomic, id=1475a045-fe75-44d1-831e-bedd86403661) +[2019-02-20T19:23:48.716Z] INFO: task-service-container/6 on ip-10-51-66-225: Uploading executor log /tmp/6d161a9d-3eba-4697-bae3-8baa85403890/tmp/test/stderr.txt (account=lifeomic, id=1475a045-fe75-44d1-831e-bedd86403661) +[2019-02-20T19:23:49.098Z] INFO: task-service-container/6 on ip-10-51-66-225: Pulling image lifeomic/kopis-task-vtools (account=lifeomic, id=1475a045-fe75-44d1-831e-bedd86403661) +[2019-02-20T19:24:04.323Z] INFO: task-service-container/6 on ip-10-51-66-225: Creating container for image lifeomic/kopis-task-vtools (account=lifeomic, id=1475a045-fe75-44d1-831e-bedd86403661, Image=lifeomic/kopis-task-vtools, AttachStdin=false, AttachStdout=true, AttachStderr=true, Tty=false, OpenStdin=false, StdinOnce=false, NetworkDisabled=true, WorkingDir=/tmp) + Cmd: [ + "vt-combo", + "-r", + "/tmp/reference/GRCh37.fa.gz", + "-i", + "/tmp/foundation.vcf", + "-o", + "/tmp/foundation.nrm.vcf" + ] + -- + HostConfig: { + "Binds": [ + "/tmp/6d161a9d-3eba-4697-bae3-8baa85403890/tmp/reference:/tmp/reference", + "/tmp/6d161a9d-3eba-4697-bae3-8baa85403890/tmp:/tmp" + ], + "Ulimits": [ + { + "Name": "nofile", + "Soft": 1024000, + "Hard": 1024000 + } + ] + } +[2019-02-20T19:24:04.834Z] INFO: task-service-container/6 on ip-10-51-66-225: Running container for image lifeomic/kopis-task-vtools (account=lifeomic, id=1475a045-fe75-44d1-831e-bedd86403661) +[2019-02-20T19:24:45.075Z] INFO: task-service-container/6 on ip-10-51-66-225: Container for image lifeomic/kopis-task-vtools finished with code 0 (account=lifeomic, id=1475a045-fe75-44d1-831e-bedd86403661) +[2019-02-20T19:24:45.075Z] INFO: task-service-container/6 on ip-10-51-66-225: Uploading executor log /tmp/6d161a9d-3eba-4697-bae3-8baa85403890/log/stdout4.txt (account=lifeomic, id=1475a045-fe75-44d1-831e-bedd86403661) +[2019-02-20T19:24:45.310Z] INFO: task-service-container/6 on ip-10-51-66-225: Uploading executor log /tmp/6d161a9d-3eba-4697-bae3-8baa85403890/log/stderr4.txt (account=lifeomic, id=1475a045-fe75-44d1-831e-bedd86403661) +[2019-02-20T19:24:45.534Z] INFO: task-service-container/6 on ip-10-51-66-225: Uploading output /tmp/6d161a9d-3eba-4697-bae3-8baa85403890/tmp/output.json (account=lifeomic, id=1475a045-fe75-44d1-831e-bedd86403661) +[2019-02-20T19:24:45.534Z] INFO: task-service-container/6 on ip-10-51-66-225: Uploading FHIR resources from /tmp/6d161a9d-3eba-4697-bae3-8baa85403890/tmp/output.json +[2019-02-20T19:24:46.491Z] INFO: task-service-container/6 on ip-10-51-66-225: Upload completed +[2019-02-20T19:24:46.492Z] INFO: task-service-container/6 on ip-10-51-66-225: Uploading output /tmp/6d161a9d-3eba-4697-bae3-8baa85403890/tmp/output.json (account=lifeomic, id=1475a045-fe75-44d1-831e-bedd86403661) +[2019-02-20T19:24:46.711Z] INFO: task-service-container/6 on ip-10-51-66-225: Uploading output /tmp/6d161a9d-3eba-4697-bae3-8baa85403890/tmp/report.pdf (account=lifeomic, id=1475a045-fe75-44d1-831e-bedd86403661) +[2019-02-20T19:24:46.974Z] INFO: task-service-container/6 on ip-10-51-66-225: Uploading output /tmp/6d161a9d-3eba-4697-bae3-8baa85403890/tmp/foundation.nrm.vcf (account=lifeomic, id=1475a045-fe75-44d1-831e-bedd86403661) +[2019-02-20T19:24:47.173Z] INFO: task-service-container/6 on ip-10-51-66-225: Kicking off index VCF job for /tmp/6d161a9d-3eba-4697-bae3-8baa85403890/tmp/foundation.nrm.vcf +[2019-02-20T19:24:47.664Z] INFO: task-service-container/6 on ip-10-51-66-225: Kicked off vcf indexing job + variantSet: { + "id": "5e7dd2c1-e62f-48e8-b02b-52eb197051c3", + "datasetId": "db3e09e9-1ecd-4976-aa5e-70ac7ada0cc3", + "name": "splice test", + "referenceSetId": "GRCh37", + "sequenceType": "somatic", + "fileId": "3d231499-ed41-4e60-8a61-77bd85c9a1a0", + "status": "INDEXING", + "patientId": "45fdb72e-2059-45aa-8e61-d31ad9156058", + "readgroupSetId": null, + "callsets": [] + } +[2019-02-20T19:24:47.665Z] INFO: task-service-container/6 on ip-10-51-66-225: Uploading execution log /tmp/task-service-container.046f87b2-4f59-496b-94f9-ef01c9372b67.log (account=lifeomic, id=1475a045-fe75-44d1-831e-bedd86403661) diff --git a/foo/tasks/1475a045-fe75-44d1-831e-bedd86403661/executor.0.stderr.txt b/foo/tasks/1475a045-fe75-44d1-831e-bedd86403661/executor.0.stderr.txt new file mode 100644 index 0000000..b4a6fb2 --- /dev/null +++ b/foo/tasks/1475a045-fe75-44d1-831e-bedd86403661/executor.0.stderr.txt @@ -0,0 +1,6 @@ +[2019-02-20 19:18:21,432] INFO [__main__.main:1046] Converting XML to FHIR with args: {"xml_file": "/tmp/SMP60684.xml", "out_file": "/tmp/output.json", "subject_id": "45fdb72e-2059-45aa-8e61-d31ad9156058", "genes": "/opt/app/refGene.hg19.txt", "file_url": "https://api.dev.lifeomic.com/v1/files/2d1ac137-91ea-4246-81f9-3e9e08ad5d1f", "vcf_out_file": "/tmp/foundation.vcf", "pdf_out_file": "/tmp/report.pdf", "fasta": "/tmp/reference/GRCh37.fa.gz", "project_id": "db3e09e9-1ecd-4976-aa5e-70ac7ada0cc3"} +[2019-02-20 19:18:21,432] INFO [__main__.unzip:33] Unzipping /tmp/reference/GRCh37.fa.gz to /tmp/reference/GRCh37.fa +[2019-02-20 19:18:54,638] INFO [__main__.unzip:38] Unzipping completed +[2019-02-20 19:23:46,955] INFO [__main__.process:1017] Created 22 FHIR resources +[2019-02-20 19:23:46,980] INFO [__main__.main:1058] Saved FHIR resources to /tmp/output.json +[2019-02-20 19:23:46,983] INFO [__main__.main:1064] Saved PDF report to /tmp/report.pdf diff --git a/foo/tasks/1475a045-fe75-44d1-831e-bedd86403661/executor.1.stderr.txt b/foo/tasks/1475a045-fe75-44d1-831e-bedd86403661/executor.1.stderr.txt new file mode 100644 index 0000000..ac51a40 --- /dev/null +++ b/foo/tasks/1475a045-fe75-44d1-831e-bedd86403661/executor.1.stderr.txt @@ -0,0 +1,71 @@ +uniq vdecompose v0.5 + +options: input VCF file /tmp/kopis-task-vtools_7e086464ba0b4999/foundation.vcf + [s] smart decomposition false (experimental) + [o] output VCF file - + +0.57 + +options: input VCF file - + [o] output VCF file - +normalize v0.5 + +options: input VCF file - + [o] output VCF file - + [w] sorting window size 10000 + [m] no fail on masked reference inconsistency false + [n] no fail on reference inconsistency true + [q] quiet false + [d] debug false + [r] reference FASTA file /tmp/kopis-task-vtools_7e086464ba0b4999/ref/GRCh37.fa.gz + + +stats: no. variants : 10 + no. biallelic variants : 10 + no. multiallelic variants : 0 + + no. additional biallelics : 0 + total no. of biallelics : 10 + +Time elapsed: 0.00s + +[W::vcf_parse] Contig '1' is not defined in the header. (Quick workaround: index the file with tabix.) +[W::vcf_parse] Contig '3' is not defined in the header. (Quick workaround: index the file with tabix.) +[W::vcf_parse] Contig '11' is not defined in the header. (Quick workaround: index the file with tabix.) +[W::vcf_parse] Contig '12' is not defined in the header. (Quick workaround: index the file with tabix.) +[W::vcf_parse] Contig '13' is not defined in the header. (Quick workaround: index the file with tabix.) +[W::vcf_parse] Contig '14' is not defined in the header. (Quick workaround: index the file with tabix.) +[W::vcf_parse] Contig '15' is not defined in the header. (Quick workaround: index the file with tabix.) +[W::vcf_parse] Contig '17' is not defined in the header. (Quick workaround: index the file with tabix.) +[W::vcf_parse] Contig '19' is not defined in the header. (Quick workaround: index the file with tabix.) + +stats: biallelic + no. left trimmed : 0 + no. right trimmed : 0 + no. left and right trimmed : 0 + no. right trimmed and left aligned : 0 + no. left aligned : 1 + + total no. biallelic normalized : 1 + + multiallelic + no. left trimmed : 0 + no. right trimmed : 0 + no. left and right trimmed : 0 + no. right trimmed and left aligned : 0 + no. left aligned : 0 + + total no. multiallelic normalized : 0 + + total no. variants normalized : 1 + total no. variants observed : 10 + total no. reference observed : 0 + +Time elapsed: 25.80s + + +stats: Total number of observed variants 10 + Total number of unique variants 10 + +Time elapsed: 0.00s + diff --git a/foo/tasks/1475a045-fe75-44d1-831e-bedd86403661/executor.1.stdout.txt b/foo/tasks/1475a045-fe75-44d1-831e-bedd86403661/executor.1.stdout.txt new file mode 100644 index 0000000..060e48c --- /dev/null +++ b/foo/tasks/1475a045-fe75-44d1-831e-bedd86403661/executor.1.stdout.txt @@ -0,0 +1,7 @@ +Args: ['/opt/app/src/run.py', 'vt-combo', '-r', '/tmp/reference/GRCh37.fa.gz', '-i', '/tmp/foundation.vcf', '-o', '/tmp/foundation.nrm.vcf'] +[execCall] mkdir /tmp/kopis-task-vtools_7e086464ba0b4999 +[execCmd] mkdir -p /tmp/kopis-task-vtools_7e086464ba0b4999; cp -f /tmp/foundation.vcf /tmp/kopis-task-vtools_7e086464ba0b4999 +[execCmd] mkdir -p /tmp/kopis-task-vtools_7e086464ba0b4999/ref; cp -f /tmp/reference/GRCh37.fa.gz /tmp/kopis-task-vtools_7e086464ba0b4999/ref +[execCmd] /opt/app/src/testVcf.sh /tmp/kopis-task-vtools_7e086464ba0b4999/foundation.vcf +[execCmd] vt decompose /tmp/kopis-task-vtools_7e086464ba0b4999/foundation.vcf | /opt/app/src/convertChrName.sh "num" - | vt normalize -n -r /tmp/kopis-task-vtools_7e086464ba0b4999/ref/GRCh37.fa.gz - | /opt/app/src/convertChrName.sh "chr" - | awk '{if ($1~/^#/) print $0; else { print $0| "sort -s -t \" \" -k1V,1 -k2n,2 -k4,5"}}' | vt uniq - > /tmp/kopis-task-vtools_7e086464ba0b4999/out-foundation.vcf +[execCmd] cp -f /tmp/kopis-task-vtools_7e086464ba0b4999/out-foundation.vcf /tmp/foundation.nrm.vcf diff --git a/foo/tasks/58c847d7-c0ab-4d82-bfe7-86ece7a5e91a/execution-log.txt b/foo/tasks/58c847d7-c0ab-4d82-bfe7-86ece7a5e91a/execution-log.txt new file mode 100644 index 0000000..b11dc1a --- /dev/null +++ b/foo/tasks/58c847d7-c0ab-4d82-bfe7-86ece7a5e91a/execution-log.txt @@ -0,0 +1,42 @@ +[2019-05-11T20:17:21.873Z] INFO: task-service-container/6 on ip-10-51-76-102: Task running on arn:aws:ecs:us-east-1:623119755067:container-instance/ab93d217-6d28-4eb9-b0bc-40b3bf705533 in cluster arn:aws:ecs:us-east-1:623119755067:cluster/task-service-v3-7k23nbyl7o1kf1f6_Batch_183d8bc1-e24f-3bc8-ad3e-b48b4ccfe131 +[2019-05-11T20:17:21.925Z] INFO: task-service-container/6 on ip-10-51-76-102: Container instance has 2048 vCPU and 7945 MB +[2019-05-11T20:17:21.926Z] INFO: task-service-container/6 on ip-10-51-76-102: Task usage (cpuUsage=0.5, memUsage=0.12586532410320955, usageFactor=0.31293266205160475) +[2019-05-11T20:17:21.928Z] INFO: task-service-container/6 on ip-10-51-76-102: dd if=/dev/zero of=/tmp/e884e050-5c11-4e81-ac41-fafcab1e9998-fs/disk-quota.ext3 count=1189144 +[2019-05-11T20:17:25.635Z] INFO: task-service-container/6 on ip-10-51-76-102: mkfs.ext3 /tmp/e884e050-5c11-4e81-ac41-fafcab1e9998-fs/disk-quota.ext3 +[2019-05-11T20:17:45.669Z] INFO: task-service-container/6 on ip-10-51-76-102: mount /tmp/e884e050-5c11-4e81-ac41-fafcab1e9998-fs/disk-quota.ext3 /tmp/e884e050-5c11-4e81-ac41-fafcab1e9998 +[2019-05-11T20:17:45.774Z] INFO: task-service-container/6 on ip-10-51-76-102: Creating output directory /tmp/e884e050-5c11-4e81-ac41-fafcab1e9998/out (account=lifeomic, id=58c847d7-c0ab-4d82-bfe7-86ece7a5e91a) +[2019-05-11T20:17:45.775Z] INFO: task-service-container/6 on ip-10-51-76-102: Task has 86400 seconds to complete +[2019-05-11T20:18:00.113Z] INFO: task-service-container/6 on ip-10-51-76-102: Image busybox already exists, skipping pull (account=lifeomic, id=58c847d7-c0ab-4d82-bfe7-86ece7a5e91a) +[2019-05-11T20:18:00.113Z] INFO: task-service-container/6 on ip-10-51-76-102: Creating container for image busybox (account=lifeomic, id=58c847d7-c0ab-4d82-bfe7-86ece7a5e91a, Image=busybox, AttachStdin=false, AttachStdout=true, AttachStderr=true, Tty=false, OpenStdin=false, StdinOnce=false, NetworkDisabled=true, WorkingDir=/tmp) + Env: [ + "LO_USER=Google_112277633572082602793", + "LO_ACCOUNT=lifeomic", + "LO_PROJECT=db3e09e9-1ecd-4976-aa5e-70ac7ada0cc3" + ] + -- + Cmd: [ + "echo", + "hello world" + ] + -- + HostConfig: { + "Binds": [ + "/tmp/e884e050-5c11-4e81-ac41-fafcab1e9998/out:/out" + ], + "Ulimits": [ + { + "Name": "nofile", + "Soft": 1024000, + "Hard": 1024000 + } + ], + "StorageOpt": { + "size": "28164M" + } + } +[2019-05-11T20:18:01.857Z] INFO: task-service-container/6 on ip-10-51-76-102: Running container for image busybox (account=lifeomic, id=58c847d7-c0ab-4d82-bfe7-86ece7a5e91a) +[2019-05-11T20:18:02.574Z] INFO: task-service-container/6 on ip-10-51-76-102: Container for image busybox finished with code 0 (account=lifeomic, id=58c847d7-c0ab-4d82-bfe7-86ece7a5e91a) +[2019-05-11T20:18:02.574Z] INFO: task-service-container/6 on ip-10-51-76-102: 86383.201 seconds left for task execution (account=lifeomic, id=58c847d7-c0ab-4d82-bfe7-86ece7a5e91a) +[2019-05-11T20:18:02.575Z] INFO: task-service-container/6 on ip-10-51-76-102: Uploading executor log /tmp/e884e050-5c11-4e81-ac41-fafcab1e9998/out/stdout.txt (account=lifeomic, id=58c847d7-c0ab-4d82-bfe7-86ece7a5e91a) +[2019-05-11T20:18:02.888Z] INFO: task-service-container/6 on ip-10-51-76-102: Uploading output /tmp/e884e050-5c11-4e81-ac41-fafcab1e9998/out (account=lifeomic, id=58c847d7-c0ab-4d82-bfe7-86ece7a5e91a) +[2019-05-11T20:18:03.184Z] INFO: task-service-container/6 on ip-10-51-76-102: Uploading execution log /tmp/task-service-container.794bee52-5266-42b0-84ab-04801ab861a9.log (account=lifeomic, id=58c847d7-c0ab-4d82-bfe7-86ece7a5e91a) diff --git a/foo/tasks/58c847d7-c0ab-4d82-bfe7-86ece7a5e91a/executor.0.stdout.txt b/foo/tasks/58c847d7-c0ab-4d82-bfe7-86ece7a5e91a/executor.0.stdout.txt new file mode 100644 index 0000000..3b18e51 --- /dev/null +++ b/foo/tasks/58c847d7-c0ab-4d82-bfe7-86ece7a5e91a/executor.0.stdout.txt @@ -0,0 +1 @@ +hello world diff --git a/foo/tasks/60d1af38-8a2b-4161-9521-5090a7ce4cc7/execution-log.txt b/foo/tasks/60d1af38-8a2b-4161-9521-5090a7ce4cc7/execution-log.txt new file mode 100644 index 0000000..ddbba48 --- /dev/null +++ b/foo/tasks/60d1af38-8a2b-4161-9521-5090a7ce4cc7/execution-log.txt @@ -0,0 +1,42 @@ +[2019-05-11T20:15:00.221Z] INFO: task-service-container/6 on ip-10-51-76-102: Task running on arn:aws:ecs:us-east-1:623119755067:container-instance/ab93d217-6d28-4eb9-b0bc-40b3bf705533 in cluster arn:aws:ecs:us-east-1:623119755067:cluster/task-service-v3-7k23nbyl7o1kf1f6_Batch_183d8bc1-e24f-3bc8-ad3e-b48b4ccfe131 +[2019-05-11T20:15:00.256Z] INFO: task-service-container/6 on ip-10-51-76-102: Container instance has 2048 vCPU and 7945 MB +[2019-05-11T20:15:00.256Z] INFO: task-service-container/6 on ip-10-51-76-102: Task usage (cpuUsage=0.5, memUsage=0.12586532410320955, usageFactor=0.31293266205160475) +[2019-05-11T20:15:00.257Z] INFO: task-service-container/6 on ip-10-51-76-102: dd if=/dev/zero of=/tmp/2fdaa4b0-8877-4db2-9b2f-dd2fa7d2d3f4-fs/disk-quota.ext3 count=1189144 +[2019-05-11T20:15:03.376Z] INFO: task-service-container/6 on ip-10-51-76-102: mkfs.ext3 /tmp/2fdaa4b0-8877-4db2-9b2f-dd2fa7d2d3f4-fs/disk-quota.ext3 +[2019-05-11T20:15:13.176Z] INFO: task-service-container/6 on ip-10-51-76-102: mount /tmp/2fdaa4b0-8877-4db2-9b2f-dd2fa7d2d3f4-fs/disk-quota.ext3 /tmp/2fdaa4b0-8877-4db2-9b2f-dd2fa7d2d3f4 +[2019-05-11T20:15:13.326Z] INFO: task-service-container/6 on ip-10-51-76-102: Creating output directory /tmp/2fdaa4b0-8877-4db2-9b2f-dd2fa7d2d3f4/out (account=lifeomic, id=60d1af38-8a2b-4161-9521-5090a7ce4cc7) +[2019-05-11T20:15:13.327Z] INFO: task-service-container/6 on ip-10-51-76-102: Task has 86400 seconds to complete +[2019-05-11T20:15:13.334Z] INFO: task-service-container/6 on ip-10-51-76-102: Pulling image busybox (account=lifeomic, id=60d1af38-8a2b-4161-9521-5090a7ce4cc7) +[2019-05-11T20:16:07.158Z] INFO: task-service-container/6 on ip-10-51-76-102: Creating container for image busybox (account=lifeomic, id=60d1af38-8a2b-4161-9521-5090a7ce4cc7, Image=busybox, AttachStdin=false, AttachStdout=true, AttachStderr=true, Tty=false, OpenStdin=false, StdinOnce=false, NetworkDisabled=true, WorkingDir=/tmp) + Env: [ + "LO_USER=Google_112277633572082602793", + "LO_ACCOUNT=lifeomic", + "LO_PROJECT=db3e09e9-1ecd-4976-aa5e-70ac7ada0cc3" + ] + -- + Cmd: [ + "echo", + "hello world" + ] + -- + HostConfig: { + "Binds": [ + "/tmp/2fdaa4b0-8877-4db2-9b2f-dd2fa7d2d3f4/out:/out" + ], + "Ulimits": [ + { + "Name": "nofile", + "Soft": 1024000, + "Hard": 1024000 + } + ], + "StorageOpt": { + "size": "28164M" + } + } +[2019-05-11T20:16:08.400Z] INFO: task-service-container/6 on ip-10-51-76-102: Running container for image busybox (account=lifeomic, id=60d1af38-8a2b-4161-9521-5090a7ce4cc7) +[2019-05-11T20:16:08.797Z] INFO: task-service-container/6 on ip-10-51-76-102: Container for image busybox finished with code 0 (account=lifeomic, id=60d1af38-8a2b-4161-9521-5090a7ce4cc7) +[2019-05-11T20:16:08.797Z] INFO: task-service-container/6 on ip-10-51-76-102: 86344.53 seconds left for task execution (account=lifeomic, id=60d1af38-8a2b-4161-9521-5090a7ce4cc7) +[2019-05-11T20:16:08.798Z] INFO: task-service-container/6 on ip-10-51-76-102: Uploading executor log /tmp/2fdaa4b0-8877-4db2-9b2f-dd2fa7d2d3f4/out/stdout.txt (account=lifeomic, id=60d1af38-8a2b-4161-9521-5090a7ce4cc7) +[2019-05-11T20:16:09.080Z] INFO: task-service-container/6 on ip-10-51-76-102: Uploading output /tmp/2fdaa4b0-8877-4db2-9b2f-dd2fa7d2d3f4/out (account=lifeomic, id=60d1af38-8a2b-4161-9521-5090a7ce4cc7) +[2019-05-11T20:16:09.388Z] INFO: task-service-container/6 on ip-10-51-76-102: Uploading execution log /tmp/task-service-container.53eb4f30-e493-495b-90dd-bf520635abb8.log (account=lifeomic, id=60d1af38-8a2b-4161-9521-5090a7ce4cc7) diff --git a/foo/tasks/60d1af38-8a2b-4161-9521-5090a7ce4cc7/executor.0.stdout.txt b/foo/tasks/60d1af38-8a2b-4161-9521-5090a7ce4cc7/executor.0.stdout.txt new file mode 100644 index 0000000..3b18e51 --- /dev/null +++ b/foo/tasks/60d1af38-8a2b-4161-9521-5090a7ce4cc7/executor.0.stdout.txt @@ -0,0 +1 @@ +hello world diff --git a/foo/tasks/66c9e1b0-866c-4c36-88a7-05e7c96780dd/execution-log.txt b/foo/tasks/66c9e1b0-866c-4c36-88a7-05e7c96780dd/execution-log.txt new file mode 100644 index 0000000..cf06520 --- /dev/null +++ b/foo/tasks/66c9e1b0-866c-4c36-88a7-05e7c96780dd/execution-log.txt @@ -0,0 +1,150 @@ +[2019-05-16T18:48:03.347Z] INFO: task-service-container/6 on ip-10-51-64-23: Here are the volumes (account=lifeomic, id=66c9e1b0-866c-4c36-88a7-05e7c96780dd, Volumes=[], Warnings=null) +[2019-05-16T18:48:03.349Z] INFO: task-service-container/6 on ip-10-51-64-23: Downloading input /tmp/72329cdf-c7ee-4c70-8de4-b23004a8469d/tmp/reference (account=lifeomic, id=66c9e1b0-866c-4c36-88a7-05e7c96780dd) +[2019-05-16T18:48:19.299Z] INFO: task-service-container/6 on ip-10-51-64-23: Downloaded /tmp/72329cdf-c7ee-4c70-8de4-b23004a8469d/tmp/reference/GRCh37.fa.gz +[2019-05-16T18:48:19.388Z] INFO: task-service-container/6 on ip-10-51-64-23: Downloaded /tmp/72329cdf-c7ee-4c70-8de4-b23004a8469d/tmp/reference/GRCh37.fa.gz.fai +[2019-05-16T18:48:19.493Z] INFO: task-service-container/6 on ip-10-51-64-23: Downloaded /tmp/72329cdf-c7ee-4c70-8de4-b23004a8469d/tmp/reference/GRCh37.fa.gz.gzi +[2019-05-16T18:48:19.566Z] INFO: task-service-container/6 on ip-10-51-64-23: Downloaded /tmp/72329cdf-c7ee-4c70-8de4-b23004a8469d/tmp/reference/upload.json +[2019-05-16T18:48:19.635Z] INFO: task-service-container/6 on ip-10-51-64-23: Downloaded /tmp/72329cdf-c7ee-4c70-8de4-b23004a8469d/tmp/reference/version.txt +[2019-05-16T18:48:19.635Z] INFO: task-service-container/6 on ip-10-51-64-23: Downloading input /tmp/72329cdf-c7ee-4c70-8de4-b23004a8469d/tmp/SMP60684.xml (account=lifeomic, id=66c9e1b0-866c-4c36-88a7-05e7c96780dd) +[2019-05-16T18:48:19.847Z] INFO: task-service-container/6 on ip-10-51-64-23: Creating output directory /tmp/72329cdf-c7ee-4c70-8de4-b23004a8469d/tmp (account=lifeomic, id=66c9e1b0-866c-4c36-88a7-05e7c96780dd) +[2019-05-16T18:48:19.848Z] INFO: task-service-container/6 on ip-10-51-64-23: Creating output directory /tmp/72329cdf-c7ee-4c70-8de4-b23004a8469d/tmp (account=lifeomic, id=66c9e1b0-866c-4c36-88a7-05e7c96780dd) +[2019-05-16T18:48:19.848Z] INFO: task-service-container/6 on ip-10-51-64-23: Creating output directory /tmp/72329cdf-c7ee-4c70-8de4-b23004a8469d/tmp (account=lifeomic, id=66c9e1b0-866c-4c36-88a7-05e7c96780dd) +[2019-05-16T18:48:19.848Z] INFO: task-service-container/6 on ip-10-51-64-23: Creating output directory /tmp/72329cdf-c7ee-4c70-8de4-b23004a8469d/tmp (account=lifeomic, id=66c9e1b0-866c-4c36-88a7-05e7c96780dd) +[2019-05-16T18:48:19.848Z] INFO: task-service-container/6 on ip-10-51-64-23: Creating output directory /tmp/72329cdf-c7ee-4c70-8de4-b23004a8469d/tmp (account=lifeomic, id=66c9e1b0-866c-4c36-88a7-05e7c96780dd) +[2019-05-16T18:48:19.848Z] INFO: task-service-container/6 on ip-10-51-64-23: Task has 86400 seconds to complete +[2019-05-16T18:48:19.851Z] INFO: task-service-container/6 on ip-10-51-64-23: Pulling image lifeomic/foundation-xml-fhir (account=lifeomic, id=66c9e1b0-866c-4c36-88a7-05e7c96780dd) +[2019-05-16T18:48:55.758Z] INFO: task-service-container/6 on ip-10-51-64-23: Creating container for image lifeomic/foundation-xml-fhir (account=lifeomic, id=66c9e1b0-866c-4c36-88a7-05e7c96780dd, Image=lifeomic/foundation-xml-fhir, AttachStdin=false, AttachStdout=true, AttachStderr=true, Tty=false, OpenStdin=false, StdinOnce=false, NetworkDisabled=true, WorkingDir=/tmp) + Env: [ + "LO_USER=Google_112277633572082602793", + "LO_ACCOUNT=lifeomic", + "LO_PROJECT=db3e09e9-1ecd-4976-aa5e-70ac7ada0cc3" + ] + -- + Cmd: [ + "-x", + "/tmp/SMP60684.xml", + "-o", + "/tmp/output.json", + "-p", + "db3e09e9-1ecd-4976-aa5e-70ac7ada0cc3", + "-r", + "/tmp/reference/GRCh37.fa.gz", + "-s", + "45fdb72e-2059-45aa-8e61-d31ad9156058", + "-f", + "https://api.dev.lifeomic.com/v1/files/66611f40-8342-4a28-a3b5-96501273e650", + "-d", + "/tmp/report.pdf", + "-v", + "/tmp/foundation.vcf" + ] + -- + HostConfig: { + "Binds": [ + "/tmp/72329cdf-c7ee-4c70-8de4-b23004a8469d/tmp/reference:/tmp/reference", + "/tmp/72329cdf-c7ee-4c70-8de4-b23004a8469d/tmp:/tmp" + ], + "Ulimits": [ + { + "Name": "nofile", + "Soft": 1024000, + "Hard": 1024000 + } + ] + } +[2019-05-16T18:48:56.096Z] INFO: task-service-container/6 on ip-10-51-64-23: Running container for image lifeomic/foundation-xml-fhir (account=lifeomic, id=66c9e1b0-866c-4c36-88a7-05e7c96780dd) +[2019-05-16T18:52:08.616Z] INFO: task-service-container/6 on ip-10-51-64-23: Container for image lifeomic/foundation-xml-fhir finished with code 0 (account=lifeomic, id=66c9e1b0-866c-4c36-88a7-05e7c96780dd) +[2019-05-16T18:52:08.616Z] INFO: task-service-container/6 on ip-10-51-64-23: 86171.232 seconds left for task execution (account=lifeomic, id=66c9e1b0-866c-4c36-88a7-05e7c96780dd) +[2019-05-16T18:52:08.617Z] INFO: task-service-container/6 on ip-10-51-64-23: Uploading executor log /tmp/72329cdf-c7ee-4c70-8de4-b23004a8469d/tmp/test/stderr.txt (account=lifeomic, id=66c9e1b0-866c-4c36-88a7-05e7c96780dd) +[2019-05-16T18:52:08.870Z] INFO: task-service-container/6 on ip-10-51-64-23: Pulling image lifeomic/kopis-task-vtools (account=lifeomic, id=66c9e1b0-866c-4c36-88a7-05e7c96780dd) +[2019-05-16T18:52:33.194Z] INFO: task-service-container/6 on ip-10-51-64-23: Creating container for image lifeomic/kopis-task-vtools (account=lifeomic, id=66c9e1b0-866c-4c36-88a7-05e7c96780dd, Image=lifeomic/kopis-task-vtools, AttachStdin=false, AttachStdout=true, AttachStderr=true, Tty=false, OpenStdin=false, StdinOnce=false, NetworkDisabled=true, WorkingDir=/tmp) + Env: [ + "LO_USER=Google_112277633572082602793", + "LO_ACCOUNT=lifeomic", + "LO_PROJECT=db3e09e9-1ecd-4976-aa5e-70ac7ada0cc3" + ] + -- + Cmd: [ + "vt-combo", + "-r", + "/tmp/reference/GRCh37.fa.gz", + "-i", + "/tmp/foundation.vcf", + "-o", + "/tmp/foundation.nrm.vcf" + ] + -- + HostConfig: { + "Binds": [ + "/tmp/72329cdf-c7ee-4c70-8de4-b23004a8469d/tmp/reference:/tmp/reference", + "/tmp/72329cdf-c7ee-4c70-8de4-b23004a8469d/tmp:/tmp" + ], + "Ulimits": [ + { + "Name": "nofile", + "Soft": 1024000, + "Hard": 1024000 + } + ] + } +[2019-05-16T18:52:33.543Z] INFO: task-service-container/6 on ip-10-51-64-23: Running container for image lifeomic/kopis-task-vtools (account=lifeomic, id=66c9e1b0-866c-4c36-88a7-05e7c96780dd) +[2019-05-16T18:52:53.781Z] INFO: task-service-container/6 on ip-10-51-64-23: Container for image lifeomic/kopis-task-vtools finished with code 0 (account=lifeomic, id=66c9e1b0-866c-4c36-88a7-05e7c96780dd) +[2019-05-16T18:52:53.781Z] INFO: task-service-container/6 on ip-10-51-64-23: 86126.319 seconds left for task execution (account=lifeomic, id=66c9e1b0-866c-4c36-88a7-05e7c96780dd) +[2019-05-16T18:52:53.782Z] INFO: task-service-container/6 on ip-10-51-64-23: Uploading executor log /tmp/72329cdf-c7ee-4c70-8de4-b23004a8469d/log/stdout4.txt (account=lifeomic, id=66c9e1b0-866c-4c36-88a7-05e7c96780dd) +[2019-05-16T18:52:54.272Z] INFO: task-service-container/6 on ip-10-51-64-23: Uploading executor log /tmp/72329cdf-c7ee-4c70-8de4-b23004a8469d/log/stderr4.txt (account=lifeomic, id=66c9e1b0-866c-4c36-88a7-05e7c96780dd) +[2019-05-16T18:52:54.431Z] INFO: task-service-container/6 on ip-10-51-64-23: Pulling image lifeomic/foundation-xml-cnv (account=lifeomic, id=66c9e1b0-866c-4c36-88a7-05e7c96780dd) +[2019-05-16T18:53:22.700Z] INFO: task-service-container/6 on ip-10-51-64-23: Creating container for image lifeomic/foundation-xml-cnv (account=lifeomic, id=66c9e1b0-866c-4c36-88a7-05e7c96780dd, Image=lifeomic/foundation-xml-cnv, AttachStdin=false, AttachStdout=true, AttachStderr=true, Tty=false, OpenStdin=false, StdinOnce=false, NetworkDisabled=true, WorkingDir=/tmp) + Env: [ + "LO_USER=Google_112277633572082602793", + "LO_ACCOUNT=lifeomic", + "LO_PROJECT=db3e09e9-1ecd-4976-aa5e-70ac7ada0cc3" + ] + -- + Cmd: [ + "-x", + "/tmp/SMP60684.xml", + "-o", + "/tmp/output.cnv" + ] + -- + HostConfig: { + "Binds": [ + "/tmp/72329cdf-c7ee-4c70-8de4-b23004a8469d/tmp/reference:/tmp/reference", + "/tmp/72329cdf-c7ee-4c70-8de4-b23004a8469d/tmp:/tmp" + ], + "Ulimits": [ + { + "Name": "nofile", + "Soft": 1024000, + "Hard": 1024000 + } + ] + } +[2019-05-16T18:53:23.108Z] INFO: task-service-container/6 on ip-10-51-64-23: Running container for image lifeomic/foundation-xml-cnv (account=lifeomic, id=66c9e1b0-866c-4c36-88a7-05e7c96780dd) +[2019-05-16T18:53:23.794Z] INFO: task-service-container/6 on ip-10-51-64-23: Container for image lifeomic/foundation-xml-cnv finished with code 0 (account=lifeomic, id=66c9e1b0-866c-4c36-88a7-05e7c96780dd) +[2019-05-16T18:53:23.795Z] INFO: task-service-container/6 on ip-10-51-64-23: 86096.95300000001 seconds left for task execution (account=lifeomic, id=66c9e1b0-866c-4c36-88a7-05e7c96780dd) +[2019-05-16T18:53:23.795Z] INFO: task-service-container/6 on ip-10-51-64-23: Uploading executor log /tmp/72329cdf-c7ee-4c70-8de4-b23004a8469d/tmp/test/stderr2.txt (account=lifeomic, id=66c9e1b0-866c-4c36-88a7-05e7c96780dd) +[2019-05-16T18:53:23.981Z] INFO: task-service-container/6 on ip-10-51-64-23: Uploading output /tmp/72329cdf-c7ee-4c70-8de4-b23004a8469d/tmp/output.json (account=lifeomic, id=66c9e1b0-866c-4c36-88a7-05e7c96780dd) +[2019-05-16T18:53:23.981Z] INFO: task-service-container/6 on ip-10-51-64-23: Uploading FHIR resources from /tmp/72329cdf-c7ee-4c70-8de4-b23004a8469d/tmp/output.json +[2019-05-16T18:53:24.599Z] INFO: task-service-container/6 on ip-10-51-64-23: Upload completed +[2019-05-16T18:53:24.600Z] INFO: task-service-container/6 on ip-10-51-64-23: Uploading output /tmp/72329cdf-c7ee-4c70-8de4-b23004a8469d/tmp/output.json (account=lifeomic, id=66c9e1b0-866c-4c36-88a7-05e7c96780dd) +[2019-05-16T18:53:24.890Z] INFO: task-service-container/6 on ip-10-51-64-23: Uploading output /tmp/72329cdf-c7ee-4c70-8de4-b23004a8469d/tmp/report.pdf (account=lifeomic, id=66c9e1b0-866c-4c36-88a7-05e7c96780dd) +[2019-05-16T18:53:25.069Z] INFO: task-service-container/6 on ip-10-51-64-23: Uploading output /tmp/72329cdf-c7ee-4c70-8de4-b23004a8469d/tmp/foundation.nrm.vcf (account=lifeomic, id=66c9e1b0-866c-4c36-88a7-05e7c96780dd) +[2019-05-16T18:53:25.228Z] INFO: task-service-container/6 on ip-10-51-64-23: Kicking off index VCF job for /tmp/72329cdf-c7ee-4c70-8de4-b23004a8469d/tmp/foundation.nrm.vcf +[2019-05-16T18:53:25.762Z] INFO: task-service-container/6 on ip-10-51-64-23: Kicked off vcf indexing job + variantSet: { + "id": "e9865f87-ef8b-483b-8e6b-7f043de500ab", + "datasetId": "db3e09e9-1ecd-4976-aa5e-70ac7ada0cc3", + "name": "splice test", + "referenceSetId": "GRCh37", + "sequenceType": "somatic", + "fileId": "3d231499-ed41-4e60-8a61-77bd85c9a1a0", + "status": "INDEXING", + "patientId": "45fdb72e-2059-45aa-8e61-d31ad9156058", + "readgroupSetId": null, + "callsets": [] + } +[2019-05-16T18:53:25.762Z] INFO: task-service-container/6 on ip-10-51-64-23: Uploading output /tmp/72329cdf-c7ee-4c70-8de4-b23004a8469d/tmp/output.cnv (account=lifeomic, id=66c9e1b0-866c-4c36-88a7-05e7c96780dd) +[2019-05-16T18:53:25.940Z] INFO: task-service-container/6 on ip-10-51-64-23: Kicking off index CNV job for /tmp/72329cdf-c7ee-4c70-8de4-b23004a8469d/tmp/output.cnv +[2019-05-16T18:53:27.640Z] INFO: splice test/6 on ip-10-51-64-23: Kicked off cnv indexing job (id=13af3a78-afec-4a64-8cd5-8740b907e4b8, datasetId=db3e09e9-1ecd-4976-aa5e-70ac7ada0cc3, fileId=b99b1224-5df2-4dce-89b0-0d7e994a055e, status=INDEXING, referenceSetId=GRCh37, sequenceType=somatic) +[2019-05-16T18:53:27.641Z] INFO: task-service-container/6 on ip-10-51-64-23: Uploading execution log /tmp/task-service-container.40a28c8d-6280-4a6b-b553-b885bb902faa.log (account=lifeomic, id=66c9e1b0-866c-4c36-88a7-05e7c96780dd) diff --git a/foo/tasks/66c9e1b0-866c-4c36-88a7-05e7c96780dd/executor.0.stderr.txt b/foo/tasks/66c9e1b0-866c-4c36-88a7-05e7c96780dd/executor.0.stderr.txt new file mode 100644 index 0000000..ebf9a28 --- /dev/null +++ b/foo/tasks/66c9e1b0-866c-4c36-88a7-05e7c96780dd/executor.0.stderr.txt @@ -0,0 +1,6 @@ +[2019-05-16 18:48:56,518] INFO [__main__.main:1109] Converting XML to FHIR with args: {"xml_file": "/tmp/SMP60684.xml", "out_file": "/tmp/output.json", "subject_id": "45fdb72e-2059-45aa-8e61-d31ad9156058", "genes": "/opt/app/refGene.hg19.txt", "file_url": "https://api.dev.lifeomic.com/v1/files/66611f40-8342-4a28-a3b5-96501273e650", "vcf_out_file": "/tmp/foundation.vcf", "pdf_out_file": "/tmp/report.pdf", "fasta": "/tmp/reference/GRCh37.fa.gz", "project_id": "db3e09e9-1ecd-4976-aa5e-70ac7ada0cc3"} +[2019-05-16 18:48:56,519] INFO [__main__.unzip:33] Unzipping /tmp/reference/GRCh37.fa.gz to /tmp/reference/GRCh37.fa +[2019-05-16 18:49:32,718] INFO [__main__.unzip:38] Unzipping completed +[2019-05-16 18:52:07,183] INFO [__main__.process:1080] Created 22 FHIR resources +[2019-05-16 18:52:07,195] INFO [__main__.main:1121] Saved FHIR resources to /tmp/output.json +[2019-05-16 18:52:07,197] INFO [__main__.main:1127] Saved PDF report to /tmp/report.pdf diff --git a/foo/tasks/66c9e1b0-866c-4c36-88a7-05e7c96780dd/executor.1.stderr.txt b/foo/tasks/66c9e1b0-866c-4c36-88a7-05e7c96780dd/executor.1.stderr.txt new file mode 100644 index 0000000..f6f1437 --- /dev/null +++ b/foo/tasks/66c9e1b0-866c-4c36-88a7-05e7c96780dd/executor.1.stderr.txt @@ -0,0 +1,71 @@ +decompose vuniq v0.57 + +options: input VCF file - + [o] output VCF file - +0.5 + +options: input VCF file /tmp/kopis-task-vtools_cf0161fb49ae46e0/foundation.vcf + [s] smart decomposition false (experimental) + [o] output VCF file - + +normalize v0.5 + +options: input VCF file - + [o] output VCF file - + [w] sorting window size 10000 + [m] no fail on masked reference inconsistency false + [n] no fail on reference inconsistency true + [q] quiet false + [d] debug false + [r] reference FASTA file /tmp/kopis-task-vtools_cf0161fb49ae46e0/ref/GRCh37.fa.gz + + +stats: no. variants : 10 + no. biallelic variants : 10 + no. multiallelic variants : 0 + + no. additional biallelics : 0 + total no. of biallelics : 10 + +Time elapsed: 0.00s + +[W::vcf_parse] Contig '1' is not defined in the header. (Quick workaround: index the file with tabix.) +[W::vcf_parse] Contig '3' is not defined in the header. (Quick workaround: index the file with tabix.) +[W::vcf_parse] Contig '11' is not defined in the header. (Quick workaround: index the file with tabix.) +[W::vcf_parse] Contig '12' is not defined in the header. (Quick workaround: index the file with tabix.) +[W::vcf_parse] Contig '13' is not defined in the header. (Quick workaround: index the file with tabix.) +[W::vcf_parse] Contig '14' is not defined in the header. (Quick workaround: index the file with tabix.) +[W::vcf_parse] Contig '15' is not defined in the header. (Quick workaround: index the file with tabix.) +[W::vcf_parse] Contig '17' is not defined in the header. (Quick workaround: index the file with tabix.) +[W::vcf_parse] Contig '19' is not defined in the header. (Quick workaround: index the file with tabix.) + +stats: biallelic + no. left trimmed : 0 + no. right trimmed : 0 + no. left and right trimmed : 0 + no. right trimmed and left aligned : 0 + no. left aligned : 1 + + total no. biallelic normalized : 1 + + multiallelic + no. left trimmed : 0 + no. right trimmed : 0 + no. left and right trimmed : 0 + no. right trimmed and left aligned : 0 + no. left aligned : 0 + + total no. multiallelic normalized : 0 + + total no. variants normalized : 1 + total no. variants observed : 10 + total no. reference observed : 0 + +Time elapsed: 18.16s + + +stats: Total number of observed variants 10 + Total number of unique variants 10 + +Time elapsed: 0.00s + diff --git a/foo/tasks/66c9e1b0-866c-4c36-88a7-05e7c96780dd/executor.1.stdout.txt b/foo/tasks/66c9e1b0-866c-4c36-88a7-05e7c96780dd/executor.1.stdout.txt new file mode 100644 index 0000000..c49d1fe --- /dev/null +++ b/foo/tasks/66c9e1b0-866c-4c36-88a7-05e7c96780dd/executor.1.stdout.txt @@ -0,0 +1,7 @@ +Args: ['/opt/app/src/run.py', 'vt-combo', '-r', '/tmp/reference/GRCh37.fa.gz', '-i', '/tmp/foundation.vcf', '-o', '/tmp/foundation.nrm.vcf'] +[execCall] mkdir /tmp/kopis-task-vtools_cf0161fb49ae46e0 +[execCmd] mkdir -p /tmp/kopis-task-vtools_cf0161fb49ae46e0; cp -f /tmp/foundation.vcf /tmp/kopis-task-vtools_cf0161fb49ae46e0 +[execCmd] mkdir -p /tmp/kopis-task-vtools_cf0161fb49ae46e0/ref; cp -f /tmp/reference/GRCh37.fa.gz /tmp/kopis-task-vtools_cf0161fb49ae46e0/ref +[execCmd] /opt/app/src/testVcf.sh /tmp/kopis-task-vtools_cf0161fb49ae46e0/foundation.vcf +[execCmd] vt decompose /tmp/kopis-task-vtools_cf0161fb49ae46e0/foundation.vcf | /opt/app/src/convertChrName.sh "num" - | vt normalize -n -r /tmp/kopis-task-vtools_cf0161fb49ae46e0/ref/GRCh37.fa.gz - | /opt/app/src/convertChrName.sh "chr" - | awk '{if ($1~/^#/) print $0; else { print $0| "sort -s -t \" \" -k1V,1 -k2n,2 -k4,5"}}' | vt uniq - > /tmp/kopis-task-vtools_cf0161fb49ae46e0/out-foundation.vcf +[execCmd] cp -f /tmp/kopis-task-vtools_cf0161fb49ae46e0/out-foundation.vcf /tmp/foundation.nrm.vcf diff --git a/foo/tasks/66c9e1b0-866c-4c36-88a7-05e7c96780dd/executor.2.stderr.txt b/foo/tasks/66c9e1b0-866c-4c36-88a7-05e7c96780dd/executor.2.stderr.txt new file mode 100644 index 0000000..9bdc92b --- /dev/null +++ b/foo/tasks/66c9e1b0-866c-4c36-88a7-05e7c96780dd/executor.2.stderr.txt @@ -0,0 +1,3 @@ +[2019-05-16 18:53:23,536] INFO [__main__.main:112] Extracting copy numbers from XML and into CNV with args: {"xml_file": "/tmp/SMP60684.xml", "out_file": "/tmp/output.cnv"} +[2019-05-16 18:53:23,568] INFO [__main__.extract_copy_numbers:64] Extracting copy numbers from xml +[2019-05-16 18:53:23,570] INFO [__main__.write_copy_numbers_to_cnv:90] Saving copy numbers to cnv file diff --git a/lib/cmds/files_cmds/download.js b/lib/cmds/files_cmds/download.js index e95e10e..a0a6589 100644 --- a/lib/cmds/files_cmds/download.js +++ b/lib/cmds/files_cmds/download.js @@ -1,22 +1,52 @@ 'use strict'; +const querystring = require('querystring'); const path = require('path'); -const { get, download } = require('../../api'); +const { get, download, list } = require('../../api'); -exports.command = 'download [destDir]'; -exports.desc = 'Download file content by '; +exports.command = 'download [destDir]'; +exports.desc = 'Download file content by '; exports.builder = yargs => { - yargs.positional('fileId', { - describe: 'The ID of the file to download.', + yargs.positional('source', { + describe: 'Either the ID of the file to download or a project ID and prefix of the form / to download a set of files from a project.', type: 'string' }).positional('destDir', { describe: 'The destination directory for the download file. Defaults to current working directory', type: 'string' + }).option('recursive', { + describe: + 'If is a project Id with an optional prefix, download all files under that prefix to the destination.', + alias: 'r', + type: 'boolean', + default: false + }).option('limit', { + describe: 'The maximum number of files to download when used with the --recursive option', + alias: 'l', + type: 'number', + default: 1000 }); }; exports.handler = async argv => { - const response = await get(argv, `/v1/files/${argv.fileId}`); + if (argv.recursive) { + const [datasetId, prefix] = argv.source.split('/'); - await download(argv, `/v1/files/${argv.fileId}?include=downloadUrl`, path.join(argv.destDir || process.cwd(), response.data.name)); + const opts = { + datasetId, + pageSize: argv.limit + }; + + if (prefix) { + opts.name = prefix; + } + + const response = await list(argv, `/v1/files?${querystring.stringify(opts)}`); + for (const item of response.data.items) { + await download(argv, `/v1/files/${item.id}?include=downloadUrl`, path.join(argv.destDir || process.cwd(), item.name)); + } + } else { + const response = await get(argv, `/v1/files/${argv.source}`); + + await download(argv, `/v1/files/${argv.source}?include=downloadUrl`, path.join(argv.destDir || process.cwd(), response.data.name)); + } }; diff --git a/test/unit/commands/file.test.js b/test/unit/commands/file.test.js index 19fdb3e..66093f7 100644 --- a/test/unit/commands/file.test.js +++ b/test/unit/commands/file.test.js @@ -207,6 +207,35 @@ test.serial.cb('The "files-download" command should download a file', t => { .parse('download fileid /dir'); }); +test.serial.cb('The "files-download" command should download a set of files from a project', t => { + listStub.onFirstCall().returns({ + data: { + items: [ + { + id: '1', + name: 'foo.txt' + } + ] + } + }); + + callback = () => { + t.is(listStub.callCount, 1); + t.is(listStub.getCall(0).args[1], '/v1/files?datasetId=projectId&pageSize=1000&name=prefix'); + + t.is(downloadSpy.callCount, 1); + t.is(downloadSpy.getCall(0).args[1], '/v1/files/1?include=downloadUrl'); + t.is(downloadSpy.getCall(0).args[2], '/dir/foo.txt'); + t.end(); + }; + + t.context.deleteFileStub = t.context.sandbox.stub(fs, 'unlinkSync').callsFake(callback); + t.context.copyFileStub = t.context.sandbox.stub(fs, 'copyFileSync').callsFake(callback); + + yargs.command(download) + .parse('download projectId/prefix /dir -r'); +}); + test.serial.cb('The "files-upload" command should upload a file', t => { const res = { data: { uploadUrl: 'https://host/upload' } }; postStub.onFirstCall().returns(res); From cf45538d02be37879d59b1b2e848649aa427c495 Mon Sep 17 00:00:00 2001 From: Mark Schroering Date: Tue, 28 May 2019 13:35:33 -0400 Subject: [PATCH 2/2] Added recursive support to the files download command --- foo/out/stderr.txt | 0 foo/out/stdout.txt | 1 - .../execution-log.txt | 42 ----- .../executor.0.stdout.txt | 1 - .../execution-log.txt | 98 ------------ .../executor.0.stderr.txt | 6 - .../executor.1.stderr.txt | 71 --------- .../executor.1.stdout.txt | 7 - .../execution-log.txt | 42 ----- .../executor.0.stdout.txt | 1 - .../execution-log.txt | 42 ----- .../executor.0.stdout.txt | 1 - .../execution-log.txt | 150 ------------------ .../executor.0.stderr.txt | 6 - .../executor.1.stderr.txt | 71 --------- .../executor.1.stdout.txt | 7 - .../executor.2.stderr.txt | 3 - 17 files changed, 549 deletions(-) delete mode 100644 foo/out/stderr.txt delete mode 100644 foo/out/stdout.txt delete mode 100644 foo/tasks/06f054f0-c1cf-4326-91bd-758adfb049e8/execution-log.txt delete mode 100644 foo/tasks/06f054f0-c1cf-4326-91bd-758adfb049e8/executor.0.stdout.txt delete mode 100644 foo/tasks/1475a045-fe75-44d1-831e-bedd86403661/execution-log.txt delete mode 100644 foo/tasks/1475a045-fe75-44d1-831e-bedd86403661/executor.0.stderr.txt delete mode 100644 foo/tasks/1475a045-fe75-44d1-831e-bedd86403661/executor.1.stderr.txt delete mode 100644 foo/tasks/1475a045-fe75-44d1-831e-bedd86403661/executor.1.stdout.txt delete mode 100644 foo/tasks/58c847d7-c0ab-4d82-bfe7-86ece7a5e91a/execution-log.txt delete mode 100644 foo/tasks/58c847d7-c0ab-4d82-bfe7-86ece7a5e91a/executor.0.stdout.txt delete mode 100644 foo/tasks/60d1af38-8a2b-4161-9521-5090a7ce4cc7/execution-log.txt delete mode 100644 foo/tasks/60d1af38-8a2b-4161-9521-5090a7ce4cc7/executor.0.stdout.txt delete mode 100644 foo/tasks/66c9e1b0-866c-4c36-88a7-05e7c96780dd/execution-log.txt delete mode 100644 foo/tasks/66c9e1b0-866c-4c36-88a7-05e7c96780dd/executor.0.stderr.txt delete mode 100644 foo/tasks/66c9e1b0-866c-4c36-88a7-05e7c96780dd/executor.1.stderr.txt delete mode 100644 foo/tasks/66c9e1b0-866c-4c36-88a7-05e7c96780dd/executor.1.stdout.txt delete mode 100644 foo/tasks/66c9e1b0-866c-4c36-88a7-05e7c96780dd/executor.2.stderr.txt diff --git a/foo/out/stderr.txt b/foo/out/stderr.txt deleted file mode 100644 index e69de29..0000000 diff --git a/foo/out/stdout.txt b/foo/out/stdout.txt deleted file mode 100644 index 3b18e51..0000000 --- a/foo/out/stdout.txt +++ /dev/null @@ -1 +0,0 @@ -hello world diff --git a/foo/tasks/06f054f0-c1cf-4326-91bd-758adfb049e8/execution-log.txt b/foo/tasks/06f054f0-c1cf-4326-91bd-758adfb049e8/execution-log.txt deleted file mode 100644 index 931bf07..0000000 --- a/foo/tasks/06f054f0-c1cf-4326-91bd-758adfb049e8/execution-log.txt +++ /dev/null @@ -1,42 +0,0 @@ -[2019-05-11T20:17:21.889Z] INFO: task-service-container/7 on ip-10-51-76-102: Task running on arn:aws:ecs:us-east-1:623119755067:container-instance/ab93d217-6d28-4eb9-b0bc-40b3bf705533 in cluster arn:aws:ecs:us-east-1:623119755067:cluster/task-service-v3-7k23nbyl7o1kf1f6_Batch_183d8bc1-e24f-3bc8-ad3e-b48b4ccfe131 -[2019-05-11T20:17:21.925Z] INFO: task-service-container/7 on ip-10-51-76-102: Container instance has 2048 vCPU and 7945 MB -[2019-05-11T20:17:21.926Z] INFO: task-service-container/7 on ip-10-51-76-102: Task usage (cpuUsage=0.5, memUsage=0.12586532410320955, usageFactor=0.31293266205160475) -[2019-05-11T20:17:21.927Z] INFO: task-service-container/7 on ip-10-51-76-102: dd if=/dev/zero of=/tmp/6fd84f00-c740-45a7-8813-b4bb1c62d56a-fs/disk-quota.ext3 count=1189144 -[2019-05-11T20:17:25.628Z] INFO: task-service-container/7 on ip-10-51-76-102: mkfs.ext3 /tmp/6fd84f00-c740-45a7-8813-b4bb1c62d56a-fs/disk-quota.ext3 -[2019-05-11T20:17:45.667Z] INFO: task-service-container/7 on ip-10-51-76-102: mount /tmp/6fd84f00-c740-45a7-8813-b4bb1c62d56a-fs/disk-quota.ext3 /tmp/6fd84f00-c740-45a7-8813-b4bb1c62d56a -[2019-05-11T20:17:45.731Z] INFO: task-service-container/7 on ip-10-51-76-102: Creating output directory /tmp/6fd84f00-c740-45a7-8813-b4bb1c62d56a/out (account=lifeomic, id=06f054f0-c1cf-4326-91bd-758adfb049e8) -[2019-05-11T20:17:45.732Z] INFO: task-service-container/7 on ip-10-51-76-102: Task has 86400 seconds to complete -[2019-05-11T20:18:01.060Z] INFO: task-service-container/7 on ip-10-51-76-102: Image busybox already exists, skipping pull (account=lifeomic, id=06f054f0-c1cf-4326-91bd-758adfb049e8) -[2019-05-11T20:18:01.061Z] INFO: task-service-container/7 on ip-10-51-76-102: Creating container for image busybox (account=lifeomic, id=06f054f0-c1cf-4326-91bd-758adfb049e8, Image=busybox, AttachStdin=false, AttachStdout=true, AttachStderr=true, Tty=false, OpenStdin=false, StdinOnce=false, NetworkDisabled=true, WorkingDir=/tmp) - Env: [ - "LO_USER=Google_112277633572082602793", - "LO_ACCOUNT=lifeomic", - "LO_PROJECT=db3e09e9-1ecd-4976-aa5e-70ac7ada0cc3" - ] - -- - Cmd: [ - "echo", - "hello world" - ] - -- - HostConfig: { - "Binds": [ - "/tmp/6fd84f00-c740-45a7-8813-b4bb1c62d56a/out:/out" - ], - "Ulimits": [ - { - "Name": "nofile", - "Soft": 1024000, - "Hard": 1024000 - } - ], - "StorageOpt": { - "size": "28164M" - } - } -[2019-05-11T20:18:02.101Z] INFO: task-service-container/7 on ip-10-51-76-102: Running container for image busybox (account=lifeomic, id=06f054f0-c1cf-4326-91bd-758adfb049e8) -[2019-05-11T20:18:02.593Z] INFO: task-service-container/7 on ip-10-51-76-102: Container for image busybox finished with code 0 (account=lifeomic, id=06f054f0-c1cf-4326-91bd-758adfb049e8) -[2019-05-11T20:18:02.594Z] INFO: task-service-container/7 on ip-10-51-76-102: 86383.138 seconds left for task execution (account=lifeomic, id=06f054f0-c1cf-4326-91bd-758adfb049e8) -[2019-05-11T20:18:02.594Z] INFO: task-service-container/7 on ip-10-51-76-102: Uploading executor log /tmp/6fd84f00-c740-45a7-8813-b4bb1c62d56a/out/stdout.txt (account=lifeomic, id=06f054f0-c1cf-4326-91bd-758adfb049e8) -[2019-05-11T20:18:02.888Z] INFO: task-service-container/7 on ip-10-51-76-102: Uploading output /tmp/6fd84f00-c740-45a7-8813-b4bb1c62d56a/out (account=lifeomic, id=06f054f0-c1cf-4326-91bd-758adfb049e8) -[2019-05-11T20:18:03.385Z] INFO: task-service-container/7 on ip-10-51-76-102: Uploading execution log /tmp/task-service-container.489ce091-2714-4cb3-a11a-c15593096405.log (account=lifeomic, id=06f054f0-c1cf-4326-91bd-758adfb049e8) diff --git a/foo/tasks/06f054f0-c1cf-4326-91bd-758adfb049e8/executor.0.stdout.txt b/foo/tasks/06f054f0-c1cf-4326-91bd-758adfb049e8/executor.0.stdout.txt deleted file mode 100644 index 3b18e51..0000000 --- a/foo/tasks/06f054f0-c1cf-4326-91bd-758adfb049e8/executor.0.stdout.txt +++ /dev/null @@ -1 +0,0 @@ -hello world diff --git a/foo/tasks/1475a045-fe75-44d1-831e-bedd86403661/execution-log.txt b/foo/tasks/1475a045-fe75-44d1-831e-bedd86403661/execution-log.txt deleted file mode 100644 index d371511..0000000 --- a/foo/tasks/1475a045-fe75-44d1-831e-bedd86403661/execution-log.txt +++ /dev/null @@ -1,98 +0,0 @@ -[2019-02-20T19:17:28.970Z] INFO: task-service-container/6 on ip-10-51-66-225: Downloading input /tmp/6d161a9d-3eba-4697-bae3-8baa85403890/tmp/reference (account=lifeomic, id=1475a045-fe75-44d1-831e-bedd86403661) -[2019-02-20T19:17:46.940Z] INFO: task-service-container/6 on ip-10-51-66-225: Downloaded /tmp/6d161a9d-3eba-4697-bae3-8baa85403890/tmp/reference/GRCh37.fa.gz -[2019-02-20T19:17:47.077Z] INFO: task-service-container/6 on ip-10-51-66-225: Downloaded /tmp/6d161a9d-3eba-4697-bae3-8baa85403890/tmp/reference/GRCh37.fa.gz.fai -[2019-02-20T19:17:47.242Z] INFO: task-service-container/6 on ip-10-51-66-225: Downloaded /tmp/6d161a9d-3eba-4697-bae3-8baa85403890/tmp/reference/GRCh37.fa.gz.gzi -[2019-02-20T19:17:47.378Z] INFO: task-service-container/6 on ip-10-51-66-225: Downloaded /tmp/6d161a9d-3eba-4697-bae3-8baa85403890/tmp/reference/upload.json -[2019-02-20T19:17:47.454Z] INFO: task-service-container/6 on ip-10-51-66-225: Downloaded /tmp/6d161a9d-3eba-4697-bae3-8baa85403890/tmp/reference/version.txt -[2019-02-20T19:17:47.454Z] INFO: task-service-container/6 on ip-10-51-66-225: Downloading input /tmp/6d161a9d-3eba-4697-bae3-8baa85403890/tmp/SMP60684.xml (account=lifeomic, id=1475a045-fe75-44d1-831e-bedd86403661) -[2019-02-20T19:17:47.649Z] INFO: task-service-container/6 on ip-10-51-66-225: Creating output directory /tmp/6d161a9d-3eba-4697-bae3-8baa85403890/tmp (account=lifeomic, id=1475a045-fe75-44d1-831e-bedd86403661) -[2019-02-20T19:17:47.649Z] INFO: task-service-container/6 on ip-10-51-66-225: Creating output directory /tmp/6d161a9d-3eba-4697-bae3-8baa85403890/tmp (account=lifeomic, id=1475a045-fe75-44d1-831e-bedd86403661) -[2019-02-20T19:17:47.649Z] INFO: task-service-container/6 on ip-10-51-66-225: Creating output directory /tmp/6d161a9d-3eba-4697-bae3-8baa85403890/tmp (account=lifeomic, id=1475a045-fe75-44d1-831e-bedd86403661) -[2019-02-20T19:17:47.649Z] INFO: task-service-container/6 on ip-10-51-66-225: Creating output directory /tmp/6d161a9d-3eba-4697-bae3-8baa85403890/tmp (account=lifeomic, id=1475a045-fe75-44d1-831e-bedd86403661) -[2019-02-20T19:17:47.654Z] INFO: task-service-container/6 on ip-10-51-66-225: Pulling image lifeomic/foundation-xml-fhir (account=lifeomic, id=1475a045-fe75-44d1-831e-bedd86403661) -[2019-02-20T19:18:20.437Z] INFO: task-service-container/6 on ip-10-51-66-225: Creating container for image lifeomic/foundation-xml-fhir (account=lifeomic, id=1475a045-fe75-44d1-831e-bedd86403661, Image=lifeomic/foundation-xml-fhir, AttachStdin=false, AttachStdout=true, AttachStderr=true, Tty=false, OpenStdin=false, StdinOnce=false, NetworkDisabled=true, WorkingDir=/tmp) - Cmd: [ - "-x", - "/tmp/SMP60684.xml", - "-o", - "/tmp/output.json", - "-p", - "db3e09e9-1ecd-4976-aa5e-70ac7ada0cc3", - "-r", - "/tmp/reference/GRCh37.fa.gz", - "-s", - "45fdb72e-2059-45aa-8e61-d31ad9156058", - "-f", - "https://api.dev.lifeomic.com/v1/files/2d1ac137-91ea-4246-81f9-3e9e08ad5d1f", - "-d", - "/tmp/report.pdf", - "-v", - "/tmp/foundation.vcf" - ] - -- - HostConfig: { - "Binds": [ - "/tmp/6d161a9d-3eba-4697-bae3-8baa85403890/tmp/reference:/tmp/reference", - "/tmp/6d161a9d-3eba-4697-bae3-8baa85403890/tmp:/tmp" - ], - "Ulimits": [ - { - "Name": "nofile", - "Soft": 1024000, - "Hard": 1024000 - } - ] - } -[2019-02-20T19:18:20.984Z] INFO: task-service-container/6 on ip-10-51-66-225: Running container for image lifeomic/foundation-xml-fhir (account=lifeomic, id=1475a045-fe75-44d1-831e-bedd86403661) -[2019-02-20T19:23:48.715Z] INFO: task-service-container/6 on ip-10-51-66-225: Container for image lifeomic/foundation-xml-fhir finished with code 0 (account=lifeomic, id=1475a045-fe75-44d1-831e-bedd86403661) -[2019-02-20T19:23:48.716Z] INFO: task-service-container/6 on ip-10-51-66-225: Uploading executor log /tmp/6d161a9d-3eba-4697-bae3-8baa85403890/tmp/test/stderr.txt (account=lifeomic, id=1475a045-fe75-44d1-831e-bedd86403661) -[2019-02-20T19:23:49.098Z] INFO: task-service-container/6 on ip-10-51-66-225: Pulling image lifeomic/kopis-task-vtools (account=lifeomic, id=1475a045-fe75-44d1-831e-bedd86403661) -[2019-02-20T19:24:04.323Z] INFO: task-service-container/6 on ip-10-51-66-225: Creating container for image lifeomic/kopis-task-vtools (account=lifeomic, id=1475a045-fe75-44d1-831e-bedd86403661, Image=lifeomic/kopis-task-vtools, AttachStdin=false, AttachStdout=true, AttachStderr=true, Tty=false, OpenStdin=false, StdinOnce=false, NetworkDisabled=true, WorkingDir=/tmp) - Cmd: [ - "vt-combo", - "-r", - "/tmp/reference/GRCh37.fa.gz", - "-i", - "/tmp/foundation.vcf", - "-o", - "/tmp/foundation.nrm.vcf" - ] - -- - HostConfig: { - "Binds": [ - "/tmp/6d161a9d-3eba-4697-bae3-8baa85403890/tmp/reference:/tmp/reference", - "/tmp/6d161a9d-3eba-4697-bae3-8baa85403890/tmp:/tmp" - ], - "Ulimits": [ - { - "Name": "nofile", - "Soft": 1024000, - "Hard": 1024000 - } - ] - } -[2019-02-20T19:24:04.834Z] INFO: task-service-container/6 on ip-10-51-66-225: Running container for image lifeomic/kopis-task-vtools (account=lifeomic, id=1475a045-fe75-44d1-831e-bedd86403661) -[2019-02-20T19:24:45.075Z] INFO: task-service-container/6 on ip-10-51-66-225: Container for image lifeomic/kopis-task-vtools finished with code 0 (account=lifeomic, id=1475a045-fe75-44d1-831e-bedd86403661) -[2019-02-20T19:24:45.075Z] INFO: task-service-container/6 on ip-10-51-66-225: Uploading executor log /tmp/6d161a9d-3eba-4697-bae3-8baa85403890/log/stdout4.txt (account=lifeomic, id=1475a045-fe75-44d1-831e-bedd86403661) -[2019-02-20T19:24:45.310Z] INFO: task-service-container/6 on ip-10-51-66-225: Uploading executor log /tmp/6d161a9d-3eba-4697-bae3-8baa85403890/log/stderr4.txt (account=lifeomic, id=1475a045-fe75-44d1-831e-bedd86403661) -[2019-02-20T19:24:45.534Z] INFO: task-service-container/6 on ip-10-51-66-225: Uploading output /tmp/6d161a9d-3eba-4697-bae3-8baa85403890/tmp/output.json (account=lifeomic, id=1475a045-fe75-44d1-831e-bedd86403661) -[2019-02-20T19:24:45.534Z] INFO: task-service-container/6 on ip-10-51-66-225: Uploading FHIR resources from /tmp/6d161a9d-3eba-4697-bae3-8baa85403890/tmp/output.json -[2019-02-20T19:24:46.491Z] INFO: task-service-container/6 on ip-10-51-66-225: Upload completed -[2019-02-20T19:24:46.492Z] INFO: task-service-container/6 on ip-10-51-66-225: Uploading output /tmp/6d161a9d-3eba-4697-bae3-8baa85403890/tmp/output.json (account=lifeomic, id=1475a045-fe75-44d1-831e-bedd86403661) -[2019-02-20T19:24:46.711Z] INFO: task-service-container/6 on ip-10-51-66-225: Uploading output /tmp/6d161a9d-3eba-4697-bae3-8baa85403890/tmp/report.pdf (account=lifeomic, id=1475a045-fe75-44d1-831e-bedd86403661) -[2019-02-20T19:24:46.974Z] INFO: task-service-container/6 on ip-10-51-66-225: Uploading output /tmp/6d161a9d-3eba-4697-bae3-8baa85403890/tmp/foundation.nrm.vcf (account=lifeomic, id=1475a045-fe75-44d1-831e-bedd86403661) -[2019-02-20T19:24:47.173Z] INFO: task-service-container/6 on ip-10-51-66-225: Kicking off index VCF job for /tmp/6d161a9d-3eba-4697-bae3-8baa85403890/tmp/foundation.nrm.vcf -[2019-02-20T19:24:47.664Z] INFO: task-service-container/6 on ip-10-51-66-225: Kicked off vcf indexing job - variantSet: { - "id": "5e7dd2c1-e62f-48e8-b02b-52eb197051c3", - "datasetId": "db3e09e9-1ecd-4976-aa5e-70ac7ada0cc3", - "name": "splice test", - "referenceSetId": "GRCh37", - "sequenceType": "somatic", - "fileId": "3d231499-ed41-4e60-8a61-77bd85c9a1a0", - "status": "INDEXING", - "patientId": "45fdb72e-2059-45aa-8e61-d31ad9156058", - "readgroupSetId": null, - "callsets": [] - } -[2019-02-20T19:24:47.665Z] INFO: task-service-container/6 on ip-10-51-66-225: Uploading execution log /tmp/task-service-container.046f87b2-4f59-496b-94f9-ef01c9372b67.log (account=lifeomic, id=1475a045-fe75-44d1-831e-bedd86403661) diff --git a/foo/tasks/1475a045-fe75-44d1-831e-bedd86403661/executor.0.stderr.txt b/foo/tasks/1475a045-fe75-44d1-831e-bedd86403661/executor.0.stderr.txt deleted file mode 100644 index b4a6fb2..0000000 --- a/foo/tasks/1475a045-fe75-44d1-831e-bedd86403661/executor.0.stderr.txt +++ /dev/null @@ -1,6 +0,0 @@ -[2019-02-20 19:18:21,432] INFO [__main__.main:1046] Converting XML to FHIR with args: {"xml_file": "/tmp/SMP60684.xml", "out_file": "/tmp/output.json", "subject_id": "45fdb72e-2059-45aa-8e61-d31ad9156058", "genes": "/opt/app/refGene.hg19.txt", "file_url": "https://api.dev.lifeomic.com/v1/files/2d1ac137-91ea-4246-81f9-3e9e08ad5d1f", "vcf_out_file": "/tmp/foundation.vcf", "pdf_out_file": "/tmp/report.pdf", "fasta": "/tmp/reference/GRCh37.fa.gz", "project_id": "db3e09e9-1ecd-4976-aa5e-70ac7ada0cc3"} -[2019-02-20 19:18:21,432] INFO [__main__.unzip:33] Unzipping /tmp/reference/GRCh37.fa.gz to /tmp/reference/GRCh37.fa -[2019-02-20 19:18:54,638] INFO [__main__.unzip:38] Unzipping completed -[2019-02-20 19:23:46,955] INFO [__main__.process:1017] Created 22 FHIR resources -[2019-02-20 19:23:46,980] INFO [__main__.main:1058] Saved FHIR resources to /tmp/output.json -[2019-02-20 19:23:46,983] INFO [__main__.main:1064] Saved PDF report to /tmp/report.pdf diff --git a/foo/tasks/1475a045-fe75-44d1-831e-bedd86403661/executor.1.stderr.txt b/foo/tasks/1475a045-fe75-44d1-831e-bedd86403661/executor.1.stderr.txt deleted file mode 100644 index ac51a40..0000000 --- a/foo/tasks/1475a045-fe75-44d1-831e-bedd86403661/executor.1.stderr.txt +++ /dev/null @@ -1,71 +0,0 @@ -uniq vdecompose v0.5 - -options: input VCF file /tmp/kopis-task-vtools_7e086464ba0b4999/foundation.vcf - [s] smart decomposition false (experimental) - [o] output VCF file - - -0.57 - -options: input VCF file - - [o] output VCF file - -normalize v0.5 - -options: input VCF file - - [o] output VCF file - - [w] sorting window size 10000 - [m] no fail on masked reference inconsistency false - [n] no fail on reference inconsistency true - [q] quiet false - [d] debug false - [r] reference FASTA file /tmp/kopis-task-vtools_7e086464ba0b4999/ref/GRCh37.fa.gz - - -stats: no. variants : 10 - no. biallelic variants : 10 - no. multiallelic variants : 0 - - no. additional biallelics : 0 - total no. of biallelics : 10 - -Time elapsed: 0.00s - -[W::vcf_parse] Contig '1' is not defined in the header. (Quick workaround: index the file with tabix.) -[W::vcf_parse] Contig '3' is not defined in the header. (Quick workaround: index the file with tabix.) -[W::vcf_parse] Contig '11' is not defined in the header. (Quick workaround: index the file with tabix.) -[W::vcf_parse] Contig '12' is not defined in the header. (Quick workaround: index the file with tabix.) -[W::vcf_parse] Contig '13' is not defined in the header. (Quick workaround: index the file with tabix.) -[W::vcf_parse] Contig '14' is not defined in the header. (Quick workaround: index the file with tabix.) -[W::vcf_parse] Contig '15' is not defined in the header. (Quick workaround: index the file with tabix.) -[W::vcf_parse] Contig '17' is not defined in the header. (Quick workaround: index the file with tabix.) -[W::vcf_parse] Contig '19' is not defined in the header. (Quick workaround: index the file with tabix.) - -stats: biallelic - no. left trimmed : 0 - no. right trimmed : 0 - no. left and right trimmed : 0 - no. right trimmed and left aligned : 0 - no. left aligned : 1 - - total no. biallelic normalized : 1 - - multiallelic - no. left trimmed : 0 - no. right trimmed : 0 - no. left and right trimmed : 0 - no. right trimmed and left aligned : 0 - no. left aligned : 0 - - total no. multiallelic normalized : 0 - - total no. variants normalized : 1 - total no. variants observed : 10 - total no. reference observed : 0 - -Time elapsed: 25.80s - - -stats: Total number of observed variants 10 - Total number of unique variants 10 - -Time elapsed: 0.00s - diff --git a/foo/tasks/1475a045-fe75-44d1-831e-bedd86403661/executor.1.stdout.txt b/foo/tasks/1475a045-fe75-44d1-831e-bedd86403661/executor.1.stdout.txt deleted file mode 100644 index 060e48c..0000000 --- a/foo/tasks/1475a045-fe75-44d1-831e-bedd86403661/executor.1.stdout.txt +++ /dev/null @@ -1,7 +0,0 @@ -Args: ['/opt/app/src/run.py', 'vt-combo', '-r', '/tmp/reference/GRCh37.fa.gz', '-i', '/tmp/foundation.vcf', '-o', '/tmp/foundation.nrm.vcf'] -[execCall] mkdir /tmp/kopis-task-vtools_7e086464ba0b4999 -[execCmd] mkdir -p /tmp/kopis-task-vtools_7e086464ba0b4999; cp -f /tmp/foundation.vcf /tmp/kopis-task-vtools_7e086464ba0b4999 -[execCmd] mkdir -p /tmp/kopis-task-vtools_7e086464ba0b4999/ref; cp -f /tmp/reference/GRCh37.fa.gz /tmp/kopis-task-vtools_7e086464ba0b4999/ref -[execCmd] /opt/app/src/testVcf.sh /tmp/kopis-task-vtools_7e086464ba0b4999/foundation.vcf -[execCmd] vt decompose /tmp/kopis-task-vtools_7e086464ba0b4999/foundation.vcf | /opt/app/src/convertChrName.sh "num" - | vt normalize -n -r /tmp/kopis-task-vtools_7e086464ba0b4999/ref/GRCh37.fa.gz - | /opt/app/src/convertChrName.sh "chr" - | awk '{if ($1~/^#/) print $0; else { print $0| "sort -s -t \" \" -k1V,1 -k2n,2 -k4,5"}}' | vt uniq - > /tmp/kopis-task-vtools_7e086464ba0b4999/out-foundation.vcf -[execCmd] cp -f /tmp/kopis-task-vtools_7e086464ba0b4999/out-foundation.vcf /tmp/foundation.nrm.vcf diff --git a/foo/tasks/58c847d7-c0ab-4d82-bfe7-86ece7a5e91a/execution-log.txt b/foo/tasks/58c847d7-c0ab-4d82-bfe7-86ece7a5e91a/execution-log.txt deleted file mode 100644 index b11dc1a..0000000 --- a/foo/tasks/58c847d7-c0ab-4d82-bfe7-86ece7a5e91a/execution-log.txt +++ /dev/null @@ -1,42 +0,0 @@ -[2019-05-11T20:17:21.873Z] INFO: task-service-container/6 on ip-10-51-76-102: Task running on arn:aws:ecs:us-east-1:623119755067:container-instance/ab93d217-6d28-4eb9-b0bc-40b3bf705533 in cluster arn:aws:ecs:us-east-1:623119755067:cluster/task-service-v3-7k23nbyl7o1kf1f6_Batch_183d8bc1-e24f-3bc8-ad3e-b48b4ccfe131 -[2019-05-11T20:17:21.925Z] INFO: task-service-container/6 on ip-10-51-76-102: Container instance has 2048 vCPU and 7945 MB -[2019-05-11T20:17:21.926Z] INFO: task-service-container/6 on ip-10-51-76-102: Task usage (cpuUsage=0.5, memUsage=0.12586532410320955, usageFactor=0.31293266205160475) -[2019-05-11T20:17:21.928Z] INFO: task-service-container/6 on ip-10-51-76-102: dd if=/dev/zero of=/tmp/e884e050-5c11-4e81-ac41-fafcab1e9998-fs/disk-quota.ext3 count=1189144 -[2019-05-11T20:17:25.635Z] INFO: task-service-container/6 on ip-10-51-76-102: mkfs.ext3 /tmp/e884e050-5c11-4e81-ac41-fafcab1e9998-fs/disk-quota.ext3 -[2019-05-11T20:17:45.669Z] INFO: task-service-container/6 on ip-10-51-76-102: mount /tmp/e884e050-5c11-4e81-ac41-fafcab1e9998-fs/disk-quota.ext3 /tmp/e884e050-5c11-4e81-ac41-fafcab1e9998 -[2019-05-11T20:17:45.774Z] INFO: task-service-container/6 on ip-10-51-76-102: Creating output directory /tmp/e884e050-5c11-4e81-ac41-fafcab1e9998/out (account=lifeomic, id=58c847d7-c0ab-4d82-bfe7-86ece7a5e91a) -[2019-05-11T20:17:45.775Z] INFO: task-service-container/6 on ip-10-51-76-102: Task has 86400 seconds to complete -[2019-05-11T20:18:00.113Z] INFO: task-service-container/6 on ip-10-51-76-102: Image busybox already exists, skipping pull (account=lifeomic, id=58c847d7-c0ab-4d82-bfe7-86ece7a5e91a) -[2019-05-11T20:18:00.113Z] INFO: task-service-container/6 on ip-10-51-76-102: Creating container for image busybox (account=lifeomic, id=58c847d7-c0ab-4d82-bfe7-86ece7a5e91a, Image=busybox, AttachStdin=false, AttachStdout=true, AttachStderr=true, Tty=false, OpenStdin=false, StdinOnce=false, NetworkDisabled=true, WorkingDir=/tmp) - Env: [ - "LO_USER=Google_112277633572082602793", - "LO_ACCOUNT=lifeomic", - "LO_PROJECT=db3e09e9-1ecd-4976-aa5e-70ac7ada0cc3" - ] - -- - Cmd: [ - "echo", - "hello world" - ] - -- - HostConfig: { - "Binds": [ - "/tmp/e884e050-5c11-4e81-ac41-fafcab1e9998/out:/out" - ], - "Ulimits": [ - { - "Name": "nofile", - "Soft": 1024000, - "Hard": 1024000 - } - ], - "StorageOpt": { - "size": "28164M" - } - } -[2019-05-11T20:18:01.857Z] INFO: task-service-container/6 on ip-10-51-76-102: Running container for image busybox (account=lifeomic, id=58c847d7-c0ab-4d82-bfe7-86ece7a5e91a) -[2019-05-11T20:18:02.574Z] INFO: task-service-container/6 on ip-10-51-76-102: Container for image busybox finished with code 0 (account=lifeomic, id=58c847d7-c0ab-4d82-bfe7-86ece7a5e91a) -[2019-05-11T20:18:02.574Z] INFO: task-service-container/6 on ip-10-51-76-102: 86383.201 seconds left for task execution (account=lifeomic, id=58c847d7-c0ab-4d82-bfe7-86ece7a5e91a) -[2019-05-11T20:18:02.575Z] INFO: task-service-container/6 on ip-10-51-76-102: Uploading executor log /tmp/e884e050-5c11-4e81-ac41-fafcab1e9998/out/stdout.txt (account=lifeomic, id=58c847d7-c0ab-4d82-bfe7-86ece7a5e91a) -[2019-05-11T20:18:02.888Z] INFO: task-service-container/6 on ip-10-51-76-102: Uploading output /tmp/e884e050-5c11-4e81-ac41-fafcab1e9998/out (account=lifeomic, id=58c847d7-c0ab-4d82-bfe7-86ece7a5e91a) -[2019-05-11T20:18:03.184Z] INFO: task-service-container/6 on ip-10-51-76-102: Uploading execution log /tmp/task-service-container.794bee52-5266-42b0-84ab-04801ab861a9.log (account=lifeomic, id=58c847d7-c0ab-4d82-bfe7-86ece7a5e91a) diff --git a/foo/tasks/58c847d7-c0ab-4d82-bfe7-86ece7a5e91a/executor.0.stdout.txt b/foo/tasks/58c847d7-c0ab-4d82-bfe7-86ece7a5e91a/executor.0.stdout.txt deleted file mode 100644 index 3b18e51..0000000 --- a/foo/tasks/58c847d7-c0ab-4d82-bfe7-86ece7a5e91a/executor.0.stdout.txt +++ /dev/null @@ -1 +0,0 @@ -hello world diff --git a/foo/tasks/60d1af38-8a2b-4161-9521-5090a7ce4cc7/execution-log.txt b/foo/tasks/60d1af38-8a2b-4161-9521-5090a7ce4cc7/execution-log.txt deleted file mode 100644 index ddbba48..0000000 --- a/foo/tasks/60d1af38-8a2b-4161-9521-5090a7ce4cc7/execution-log.txt +++ /dev/null @@ -1,42 +0,0 @@ -[2019-05-11T20:15:00.221Z] INFO: task-service-container/6 on ip-10-51-76-102: Task running on arn:aws:ecs:us-east-1:623119755067:container-instance/ab93d217-6d28-4eb9-b0bc-40b3bf705533 in cluster arn:aws:ecs:us-east-1:623119755067:cluster/task-service-v3-7k23nbyl7o1kf1f6_Batch_183d8bc1-e24f-3bc8-ad3e-b48b4ccfe131 -[2019-05-11T20:15:00.256Z] INFO: task-service-container/6 on ip-10-51-76-102: Container instance has 2048 vCPU and 7945 MB -[2019-05-11T20:15:00.256Z] INFO: task-service-container/6 on ip-10-51-76-102: Task usage (cpuUsage=0.5, memUsage=0.12586532410320955, usageFactor=0.31293266205160475) -[2019-05-11T20:15:00.257Z] INFO: task-service-container/6 on ip-10-51-76-102: dd if=/dev/zero of=/tmp/2fdaa4b0-8877-4db2-9b2f-dd2fa7d2d3f4-fs/disk-quota.ext3 count=1189144 -[2019-05-11T20:15:03.376Z] INFO: task-service-container/6 on ip-10-51-76-102: mkfs.ext3 /tmp/2fdaa4b0-8877-4db2-9b2f-dd2fa7d2d3f4-fs/disk-quota.ext3 -[2019-05-11T20:15:13.176Z] INFO: task-service-container/6 on ip-10-51-76-102: mount /tmp/2fdaa4b0-8877-4db2-9b2f-dd2fa7d2d3f4-fs/disk-quota.ext3 /tmp/2fdaa4b0-8877-4db2-9b2f-dd2fa7d2d3f4 -[2019-05-11T20:15:13.326Z] INFO: task-service-container/6 on ip-10-51-76-102: Creating output directory /tmp/2fdaa4b0-8877-4db2-9b2f-dd2fa7d2d3f4/out (account=lifeomic, id=60d1af38-8a2b-4161-9521-5090a7ce4cc7) -[2019-05-11T20:15:13.327Z] INFO: task-service-container/6 on ip-10-51-76-102: Task has 86400 seconds to complete -[2019-05-11T20:15:13.334Z] INFO: task-service-container/6 on ip-10-51-76-102: Pulling image busybox (account=lifeomic, id=60d1af38-8a2b-4161-9521-5090a7ce4cc7) -[2019-05-11T20:16:07.158Z] INFO: task-service-container/6 on ip-10-51-76-102: Creating container for image busybox (account=lifeomic, id=60d1af38-8a2b-4161-9521-5090a7ce4cc7, Image=busybox, AttachStdin=false, AttachStdout=true, AttachStderr=true, Tty=false, OpenStdin=false, StdinOnce=false, NetworkDisabled=true, WorkingDir=/tmp) - Env: [ - "LO_USER=Google_112277633572082602793", - "LO_ACCOUNT=lifeomic", - "LO_PROJECT=db3e09e9-1ecd-4976-aa5e-70ac7ada0cc3" - ] - -- - Cmd: [ - "echo", - "hello world" - ] - -- - HostConfig: { - "Binds": [ - "/tmp/2fdaa4b0-8877-4db2-9b2f-dd2fa7d2d3f4/out:/out" - ], - "Ulimits": [ - { - "Name": "nofile", - "Soft": 1024000, - "Hard": 1024000 - } - ], - "StorageOpt": { - "size": "28164M" - } - } -[2019-05-11T20:16:08.400Z] INFO: task-service-container/6 on ip-10-51-76-102: Running container for image busybox (account=lifeomic, id=60d1af38-8a2b-4161-9521-5090a7ce4cc7) -[2019-05-11T20:16:08.797Z] INFO: task-service-container/6 on ip-10-51-76-102: Container for image busybox finished with code 0 (account=lifeomic, id=60d1af38-8a2b-4161-9521-5090a7ce4cc7) -[2019-05-11T20:16:08.797Z] INFO: task-service-container/6 on ip-10-51-76-102: 86344.53 seconds left for task execution (account=lifeomic, id=60d1af38-8a2b-4161-9521-5090a7ce4cc7) -[2019-05-11T20:16:08.798Z] INFO: task-service-container/6 on ip-10-51-76-102: Uploading executor log /tmp/2fdaa4b0-8877-4db2-9b2f-dd2fa7d2d3f4/out/stdout.txt (account=lifeomic, id=60d1af38-8a2b-4161-9521-5090a7ce4cc7) -[2019-05-11T20:16:09.080Z] INFO: task-service-container/6 on ip-10-51-76-102: Uploading output /tmp/2fdaa4b0-8877-4db2-9b2f-dd2fa7d2d3f4/out (account=lifeomic, id=60d1af38-8a2b-4161-9521-5090a7ce4cc7) -[2019-05-11T20:16:09.388Z] INFO: task-service-container/6 on ip-10-51-76-102: Uploading execution log /tmp/task-service-container.53eb4f30-e493-495b-90dd-bf520635abb8.log (account=lifeomic, id=60d1af38-8a2b-4161-9521-5090a7ce4cc7) diff --git a/foo/tasks/60d1af38-8a2b-4161-9521-5090a7ce4cc7/executor.0.stdout.txt b/foo/tasks/60d1af38-8a2b-4161-9521-5090a7ce4cc7/executor.0.stdout.txt deleted file mode 100644 index 3b18e51..0000000 --- a/foo/tasks/60d1af38-8a2b-4161-9521-5090a7ce4cc7/executor.0.stdout.txt +++ /dev/null @@ -1 +0,0 @@ -hello world diff --git a/foo/tasks/66c9e1b0-866c-4c36-88a7-05e7c96780dd/execution-log.txt b/foo/tasks/66c9e1b0-866c-4c36-88a7-05e7c96780dd/execution-log.txt deleted file mode 100644 index cf06520..0000000 --- a/foo/tasks/66c9e1b0-866c-4c36-88a7-05e7c96780dd/execution-log.txt +++ /dev/null @@ -1,150 +0,0 @@ -[2019-05-16T18:48:03.347Z] INFO: task-service-container/6 on ip-10-51-64-23: Here are the volumes (account=lifeomic, id=66c9e1b0-866c-4c36-88a7-05e7c96780dd, Volumes=[], Warnings=null) -[2019-05-16T18:48:03.349Z] INFO: task-service-container/6 on ip-10-51-64-23: Downloading input /tmp/72329cdf-c7ee-4c70-8de4-b23004a8469d/tmp/reference (account=lifeomic, id=66c9e1b0-866c-4c36-88a7-05e7c96780dd) -[2019-05-16T18:48:19.299Z] INFO: task-service-container/6 on ip-10-51-64-23: Downloaded /tmp/72329cdf-c7ee-4c70-8de4-b23004a8469d/tmp/reference/GRCh37.fa.gz -[2019-05-16T18:48:19.388Z] INFO: task-service-container/6 on ip-10-51-64-23: Downloaded /tmp/72329cdf-c7ee-4c70-8de4-b23004a8469d/tmp/reference/GRCh37.fa.gz.fai -[2019-05-16T18:48:19.493Z] INFO: task-service-container/6 on ip-10-51-64-23: Downloaded /tmp/72329cdf-c7ee-4c70-8de4-b23004a8469d/tmp/reference/GRCh37.fa.gz.gzi -[2019-05-16T18:48:19.566Z] INFO: task-service-container/6 on ip-10-51-64-23: Downloaded /tmp/72329cdf-c7ee-4c70-8de4-b23004a8469d/tmp/reference/upload.json -[2019-05-16T18:48:19.635Z] INFO: task-service-container/6 on ip-10-51-64-23: Downloaded /tmp/72329cdf-c7ee-4c70-8de4-b23004a8469d/tmp/reference/version.txt -[2019-05-16T18:48:19.635Z] INFO: task-service-container/6 on ip-10-51-64-23: Downloading input /tmp/72329cdf-c7ee-4c70-8de4-b23004a8469d/tmp/SMP60684.xml (account=lifeomic, id=66c9e1b0-866c-4c36-88a7-05e7c96780dd) -[2019-05-16T18:48:19.847Z] INFO: task-service-container/6 on ip-10-51-64-23: Creating output directory /tmp/72329cdf-c7ee-4c70-8de4-b23004a8469d/tmp (account=lifeomic, id=66c9e1b0-866c-4c36-88a7-05e7c96780dd) -[2019-05-16T18:48:19.848Z] INFO: task-service-container/6 on ip-10-51-64-23: Creating output directory /tmp/72329cdf-c7ee-4c70-8de4-b23004a8469d/tmp (account=lifeomic, id=66c9e1b0-866c-4c36-88a7-05e7c96780dd) -[2019-05-16T18:48:19.848Z] INFO: task-service-container/6 on ip-10-51-64-23: Creating output directory /tmp/72329cdf-c7ee-4c70-8de4-b23004a8469d/tmp (account=lifeomic, id=66c9e1b0-866c-4c36-88a7-05e7c96780dd) -[2019-05-16T18:48:19.848Z] INFO: task-service-container/6 on ip-10-51-64-23: Creating output directory /tmp/72329cdf-c7ee-4c70-8de4-b23004a8469d/tmp (account=lifeomic, id=66c9e1b0-866c-4c36-88a7-05e7c96780dd) -[2019-05-16T18:48:19.848Z] INFO: task-service-container/6 on ip-10-51-64-23: Creating output directory /tmp/72329cdf-c7ee-4c70-8de4-b23004a8469d/tmp (account=lifeomic, id=66c9e1b0-866c-4c36-88a7-05e7c96780dd) -[2019-05-16T18:48:19.848Z] INFO: task-service-container/6 on ip-10-51-64-23: Task has 86400 seconds to complete -[2019-05-16T18:48:19.851Z] INFO: task-service-container/6 on ip-10-51-64-23: Pulling image lifeomic/foundation-xml-fhir (account=lifeomic, id=66c9e1b0-866c-4c36-88a7-05e7c96780dd) -[2019-05-16T18:48:55.758Z] INFO: task-service-container/6 on ip-10-51-64-23: Creating container for image lifeomic/foundation-xml-fhir (account=lifeomic, id=66c9e1b0-866c-4c36-88a7-05e7c96780dd, Image=lifeomic/foundation-xml-fhir, AttachStdin=false, AttachStdout=true, AttachStderr=true, Tty=false, OpenStdin=false, StdinOnce=false, NetworkDisabled=true, WorkingDir=/tmp) - Env: [ - "LO_USER=Google_112277633572082602793", - "LO_ACCOUNT=lifeomic", - "LO_PROJECT=db3e09e9-1ecd-4976-aa5e-70ac7ada0cc3" - ] - -- - Cmd: [ - "-x", - "/tmp/SMP60684.xml", - "-o", - "/tmp/output.json", - "-p", - "db3e09e9-1ecd-4976-aa5e-70ac7ada0cc3", - "-r", - "/tmp/reference/GRCh37.fa.gz", - "-s", - "45fdb72e-2059-45aa-8e61-d31ad9156058", - "-f", - "https://api.dev.lifeomic.com/v1/files/66611f40-8342-4a28-a3b5-96501273e650", - "-d", - "/tmp/report.pdf", - "-v", - "/tmp/foundation.vcf" - ] - -- - HostConfig: { - "Binds": [ - "/tmp/72329cdf-c7ee-4c70-8de4-b23004a8469d/tmp/reference:/tmp/reference", - "/tmp/72329cdf-c7ee-4c70-8de4-b23004a8469d/tmp:/tmp" - ], - "Ulimits": [ - { - "Name": "nofile", - "Soft": 1024000, - "Hard": 1024000 - } - ] - } -[2019-05-16T18:48:56.096Z] INFO: task-service-container/6 on ip-10-51-64-23: Running container for image lifeomic/foundation-xml-fhir (account=lifeomic, id=66c9e1b0-866c-4c36-88a7-05e7c96780dd) -[2019-05-16T18:52:08.616Z] INFO: task-service-container/6 on ip-10-51-64-23: Container for image lifeomic/foundation-xml-fhir finished with code 0 (account=lifeomic, id=66c9e1b0-866c-4c36-88a7-05e7c96780dd) -[2019-05-16T18:52:08.616Z] INFO: task-service-container/6 on ip-10-51-64-23: 86171.232 seconds left for task execution (account=lifeomic, id=66c9e1b0-866c-4c36-88a7-05e7c96780dd) -[2019-05-16T18:52:08.617Z] INFO: task-service-container/6 on ip-10-51-64-23: Uploading executor log /tmp/72329cdf-c7ee-4c70-8de4-b23004a8469d/tmp/test/stderr.txt (account=lifeomic, id=66c9e1b0-866c-4c36-88a7-05e7c96780dd) -[2019-05-16T18:52:08.870Z] INFO: task-service-container/6 on ip-10-51-64-23: Pulling image lifeomic/kopis-task-vtools (account=lifeomic, id=66c9e1b0-866c-4c36-88a7-05e7c96780dd) -[2019-05-16T18:52:33.194Z] INFO: task-service-container/6 on ip-10-51-64-23: Creating container for image lifeomic/kopis-task-vtools (account=lifeomic, id=66c9e1b0-866c-4c36-88a7-05e7c96780dd, Image=lifeomic/kopis-task-vtools, AttachStdin=false, AttachStdout=true, AttachStderr=true, Tty=false, OpenStdin=false, StdinOnce=false, NetworkDisabled=true, WorkingDir=/tmp) - Env: [ - "LO_USER=Google_112277633572082602793", - "LO_ACCOUNT=lifeomic", - "LO_PROJECT=db3e09e9-1ecd-4976-aa5e-70ac7ada0cc3" - ] - -- - Cmd: [ - "vt-combo", - "-r", - "/tmp/reference/GRCh37.fa.gz", - "-i", - "/tmp/foundation.vcf", - "-o", - "/tmp/foundation.nrm.vcf" - ] - -- - HostConfig: { - "Binds": [ - "/tmp/72329cdf-c7ee-4c70-8de4-b23004a8469d/tmp/reference:/tmp/reference", - "/tmp/72329cdf-c7ee-4c70-8de4-b23004a8469d/tmp:/tmp" - ], - "Ulimits": [ - { - "Name": "nofile", - "Soft": 1024000, - "Hard": 1024000 - } - ] - } -[2019-05-16T18:52:33.543Z] INFO: task-service-container/6 on ip-10-51-64-23: Running container for image lifeomic/kopis-task-vtools (account=lifeomic, id=66c9e1b0-866c-4c36-88a7-05e7c96780dd) -[2019-05-16T18:52:53.781Z] INFO: task-service-container/6 on ip-10-51-64-23: Container for image lifeomic/kopis-task-vtools finished with code 0 (account=lifeomic, id=66c9e1b0-866c-4c36-88a7-05e7c96780dd) -[2019-05-16T18:52:53.781Z] INFO: task-service-container/6 on ip-10-51-64-23: 86126.319 seconds left for task execution (account=lifeomic, id=66c9e1b0-866c-4c36-88a7-05e7c96780dd) -[2019-05-16T18:52:53.782Z] INFO: task-service-container/6 on ip-10-51-64-23: Uploading executor log /tmp/72329cdf-c7ee-4c70-8de4-b23004a8469d/log/stdout4.txt (account=lifeomic, id=66c9e1b0-866c-4c36-88a7-05e7c96780dd) -[2019-05-16T18:52:54.272Z] INFO: task-service-container/6 on ip-10-51-64-23: Uploading executor log /tmp/72329cdf-c7ee-4c70-8de4-b23004a8469d/log/stderr4.txt (account=lifeomic, id=66c9e1b0-866c-4c36-88a7-05e7c96780dd) -[2019-05-16T18:52:54.431Z] INFO: task-service-container/6 on ip-10-51-64-23: Pulling image lifeomic/foundation-xml-cnv (account=lifeomic, id=66c9e1b0-866c-4c36-88a7-05e7c96780dd) -[2019-05-16T18:53:22.700Z] INFO: task-service-container/6 on ip-10-51-64-23: Creating container for image lifeomic/foundation-xml-cnv (account=lifeomic, id=66c9e1b0-866c-4c36-88a7-05e7c96780dd, Image=lifeomic/foundation-xml-cnv, AttachStdin=false, AttachStdout=true, AttachStderr=true, Tty=false, OpenStdin=false, StdinOnce=false, NetworkDisabled=true, WorkingDir=/tmp) - Env: [ - "LO_USER=Google_112277633572082602793", - "LO_ACCOUNT=lifeomic", - "LO_PROJECT=db3e09e9-1ecd-4976-aa5e-70ac7ada0cc3" - ] - -- - Cmd: [ - "-x", - "/tmp/SMP60684.xml", - "-o", - "/tmp/output.cnv" - ] - -- - HostConfig: { - "Binds": [ - "/tmp/72329cdf-c7ee-4c70-8de4-b23004a8469d/tmp/reference:/tmp/reference", - "/tmp/72329cdf-c7ee-4c70-8de4-b23004a8469d/tmp:/tmp" - ], - "Ulimits": [ - { - "Name": "nofile", - "Soft": 1024000, - "Hard": 1024000 - } - ] - } -[2019-05-16T18:53:23.108Z] INFO: task-service-container/6 on ip-10-51-64-23: Running container for image lifeomic/foundation-xml-cnv (account=lifeomic, id=66c9e1b0-866c-4c36-88a7-05e7c96780dd) -[2019-05-16T18:53:23.794Z] INFO: task-service-container/6 on ip-10-51-64-23: Container for image lifeomic/foundation-xml-cnv finished with code 0 (account=lifeomic, id=66c9e1b0-866c-4c36-88a7-05e7c96780dd) -[2019-05-16T18:53:23.795Z] INFO: task-service-container/6 on ip-10-51-64-23: 86096.95300000001 seconds left for task execution (account=lifeomic, id=66c9e1b0-866c-4c36-88a7-05e7c96780dd) -[2019-05-16T18:53:23.795Z] INFO: task-service-container/6 on ip-10-51-64-23: Uploading executor log /tmp/72329cdf-c7ee-4c70-8de4-b23004a8469d/tmp/test/stderr2.txt (account=lifeomic, id=66c9e1b0-866c-4c36-88a7-05e7c96780dd) -[2019-05-16T18:53:23.981Z] INFO: task-service-container/6 on ip-10-51-64-23: Uploading output /tmp/72329cdf-c7ee-4c70-8de4-b23004a8469d/tmp/output.json (account=lifeomic, id=66c9e1b0-866c-4c36-88a7-05e7c96780dd) -[2019-05-16T18:53:23.981Z] INFO: task-service-container/6 on ip-10-51-64-23: Uploading FHIR resources from /tmp/72329cdf-c7ee-4c70-8de4-b23004a8469d/tmp/output.json -[2019-05-16T18:53:24.599Z] INFO: task-service-container/6 on ip-10-51-64-23: Upload completed -[2019-05-16T18:53:24.600Z] INFO: task-service-container/6 on ip-10-51-64-23: Uploading output /tmp/72329cdf-c7ee-4c70-8de4-b23004a8469d/tmp/output.json (account=lifeomic, id=66c9e1b0-866c-4c36-88a7-05e7c96780dd) -[2019-05-16T18:53:24.890Z] INFO: task-service-container/6 on ip-10-51-64-23: Uploading output /tmp/72329cdf-c7ee-4c70-8de4-b23004a8469d/tmp/report.pdf (account=lifeomic, id=66c9e1b0-866c-4c36-88a7-05e7c96780dd) -[2019-05-16T18:53:25.069Z] INFO: task-service-container/6 on ip-10-51-64-23: Uploading output /tmp/72329cdf-c7ee-4c70-8de4-b23004a8469d/tmp/foundation.nrm.vcf (account=lifeomic, id=66c9e1b0-866c-4c36-88a7-05e7c96780dd) -[2019-05-16T18:53:25.228Z] INFO: task-service-container/6 on ip-10-51-64-23: Kicking off index VCF job for /tmp/72329cdf-c7ee-4c70-8de4-b23004a8469d/tmp/foundation.nrm.vcf -[2019-05-16T18:53:25.762Z] INFO: task-service-container/6 on ip-10-51-64-23: Kicked off vcf indexing job - variantSet: { - "id": "e9865f87-ef8b-483b-8e6b-7f043de500ab", - "datasetId": "db3e09e9-1ecd-4976-aa5e-70ac7ada0cc3", - "name": "splice test", - "referenceSetId": "GRCh37", - "sequenceType": "somatic", - "fileId": "3d231499-ed41-4e60-8a61-77bd85c9a1a0", - "status": "INDEXING", - "patientId": "45fdb72e-2059-45aa-8e61-d31ad9156058", - "readgroupSetId": null, - "callsets": [] - } -[2019-05-16T18:53:25.762Z] INFO: task-service-container/6 on ip-10-51-64-23: Uploading output /tmp/72329cdf-c7ee-4c70-8de4-b23004a8469d/tmp/output.cnv (account=lifeomic, id=66c9e1b0-866c-4c36-88a7-05e7c96780dd) -[2019-05-16T18:53:25.940Z] INFO: task-service-container/6 on ip-10-51-64-23: Kicking off index CNV job for /tmp/72329cdf-c7ee-4c70-8de4-b23004a8469d/tmp/output.cnv -[2019-05-16T18:53:27.640Z] INFO: splice test/6 on ip-10-51-64-23: Kicked off cnv indexing job (id=13af3a78-afec-4a64-8cd5-8740b907e4b8, datasetId=db3e09e9-1ecd-4976-aa5e-70ac7ada0cc3, fileId=b99b1224-5df2-4dce-89b0-0d7e994a055e, status=INDEXING, referenceSetId=GRCh37, sequenceType=somatic) -[2019-05-16T18:53:27.641Z] INFO: task-service-container/6 on ip-10-51-64-23: Uploading execution log /tmp/task-service-container.40a28c8d-6280-4a6b-b553-b885bb902faa.log (account=lifeomic, id=66c9e1b0-866c-4c36-88a7-05e7c96780dd) diff --git a/foo/tasks/66c9e1b0-866c-4c36-88a7-05e7c96780dd/executor.0.stderr.txt b/foo/tasks/66c9e1b0-866c-4c36-88a7-05e7c96780dd/executor.0.stderr.txt deleted file mode 100644 index ebf9a28..0000000 --- a/foo/tasks/66c9e1b0-866c-4c36-88a7-05e7c96780dd/executor.0.stderr.txt +++ /dev/null @@ -1,6 +0,0 @@ -[2019-05-16 18:48:56,518] INFO [__main__.main:1109] Converting XML to FHIR with args: {"xml_file": "/tmp/SMP60684.xml", "out_file": "/tmp/output.json", "subject_id": "45fdb72e-2059-45aa-8e61-d31ad9156058", "genes": "/opt/app/refGene.hg19.txt", "file_url": "https://api.dev.lifeomic.com/v1/files/66611f40-8342-4a28-a3b5-96501273e650", "vcf_out_file": "/tmp/foundation.vcf", "pdf_out_file": "/tmp/report.pdf", "fasta": "/tmp/reference/GRCh37.fa.gz", "project_id": "db3e09e9-1ecd-4976-aa5e-70ac7ada0cc3"} -[2019-05-16 18:48:56,519] INFO [__main__.unzip:33] Unzipping /tmp/reference/GRCh37.fa.gz to /tmp/reference/GRCh37.fa -[2019-05-16 18:49:32,718] INFO [__main__.unzip:38] Unzipping completed -[2019-05-16 18:52:07,183] INFO [__main__.process:1080] Created 22 FHIR resources -[2019-05-16 18:52:07,195] INFO [__main__.main:1121] Saved FHIR resources to /tmp/output.json -[2019-05-16 18:52:07,197] INFO [__main__.main:1127] Saved PDF report to /tmp/report.pdf diff --git a/foo/tasks/66c9e1b0-866c-4c36-88a7-05e7c96780dd/executor.1.stderr.txt b/foo/tasks/66c9e1b0-866c-4c36-88a7-05e7c96780dd/executor.1.stderr.txt deleted file mode 100644 index f6f1437..0000000 --- a/foo/tasks/66c9e1b0-866c-4c36-88a7-05e7c96780dd/executor.1.stderr.txt +++ /dev/null @@ -1,71 +0,0 @@ -decompose vuniq v0.57 - -options: input VCF file - - [o] output VCF file - -0.5 - -options: input VCF file /tmp/kopis-task-vtools_cf0161fb49ae46e0/foundation.vcf - [s] smart decomposition false (experimental) - [o] output VCF file - - -normalize v0.5 - -options: input VCF file - - [o] output VCF file - - [w] sorting window size 10000 - [m] no fail on masked reference inconsistency false - [n] no fail on reference inconsistency true - [q] quiet false - [d] debug false - [r] reference FASTA file /tmp/kopis-task-vtools_cf0161fb49ae46e0/ref/GRCh37.fa.gz - - -stats: no. variants : 10 - no. biallelic variants : 10 - no. multiallelic variants : 0 - - no. additional biallelics : 0 - total no. of biallelics : 10 - -Time elapsed: 0.00s - -[W::vcf_parse] Contig '1' is not defined in the header. (Quick workaround: index the file with tabix.) -[W::vcf_parse] Contig '3' is not defined in the header. (Quick workaround: index the file with tabix.) -[W::vcf_parse] Contig '11' is not defined in the header. (Quick workaround: index the file with tabix.) -[W::vcf_parse] Contig '12' is not defined in the header. (Quick workaround: index the file with tabix.) -[W::vcf_parse] Contig '13' is not defined in the header. (Quick workaround: index the file with tabix.) -[W::vcf_parse] Contig '14' is not defined in the header. (Quick workaround: index the file with tabix.) -[W::vcf_parse] Contig '15' is not defined in the header. (Quick workaround: index the file with tabix.) -[W::vcf_parse] Contig '17' is not defined in the header. (Quick workaround: index the file with tabix.) -[W::vcf_parse] Contig '19' is not defined in the header. (Quick workaround: index the file with tabix.) - -stats: biallelic - no. left trimmed : 0 - no. right trimmed : 0 - no. left and right trimmed : 0 - no. right trimmed and left aligned : 0 - no. left aligned : 1 - - total no. biallelic normalized : 1 - - multiallelic - no. left trimmed : 0 - no. right trimmed : 0 - no. left and right trimmed : 0 - no. right trimmed and left aligned : 0 - no. left aligned : 0 - - total no. multiallelic normalized : 0 - - total no. variants normalized : 1 - total no. variants observed : 10 - total no. reference observed : 0 - -Time elapsed: 18.16s - - -stats: Total number of observed variants 10 - Total number of unique variants 10 - -Time elapsed: 0.00s - diff --git a/foo/tasks/66c9e1b0-866c-4c36-88a7-05e7c96780dd/executor.1.stdout.txt b/foo/tasks/66c9e1b0-866c-4c36-88a7-05e7c96780dd/executor.1.stdout.txt deleted file mode 100644 index c49d1fe..0000000 --- a/foo/tasks/66c9e1b0-866c-4c36-88a7-05e7c96780dd/executor.1.stdout.txt +++ /dev/null @@ -1,7 +0,0 @@ -Args: ['/opt/app/src/run.py', 'vt-combo', '-r', '/tmp/reference/GRCh37.fa.gz', '-i', '/tmp/foundation.vcf', '-o', '/tmp/foundation.nrm.vcf'] -[execCall] mkdir /tmp/kopis-task-vtools_cf0161fb49ae46e0 -[execCmd] mkdir -p /tmp/kopis-task-vtools_cf0161fb49ae46e0; cp -f /tmp/foundation.vcf /tmp/kopis-task-vtools_cf0161fb49ae46e0 -[execCmd] mkdir -p /tmp/kopis-task-vtools_cf0161fb49ae46e0/ref; cp -f /tmp/reference/GRCh37.fa.gz /tmp/kopis-task-vtools_cf0161fb49ae46e0/ref -[execCmd] /opt/app/src/testVcf.sh /tmp/kopis-task-vtools_cf0161fb49ae46e0/foundation.vcf -[execCmd] vt decompose /tmp/kopis-task-vtools_cf0161fb49ae46e0/foundation.vcf | /opt/app/src/convertChrName.sh "num" - | vt normalize -n -r /tmp/kopis-task-vtools_cf0161fb49ae46e0/ref/GRCh37.fa.gz - | /opt/app/src/convertChrName.sh "chr" - | awk '{if ($1~/^#/) print $0; else { print $0| "sort -s -t \" \" -k1V,1 -k2n,2 -k4,5"}}' | vt uniq - > /tmp/kopis-task-vtools_cf0161fb49ae46e0/out-foundation.vcf -[execCmd] cp -f /tmp/kopis-task-vtools_cf0161fb49ae46e0/out-foundation.vcf /tmp/foundation.nrm.vcf diff --git a/foo/tasks/66c9e1b0-866c-4c36-88a7-05e7c96780dd/executor.2.stderr.txt b/foo/tasks/66c9e1b0-866c-4c36-88a7-05e7c96780dd/executor.2.stderr.txt deleted file mode 100644 index 9bdc92b..0000000 --- a/foo/tasks/66c9e1b0-866c-4c36-88a7-05e7c96780dd/executor.2.stderr.txt +++ /dev/null @@ -1,3 +0,0 @@ -[2019-05-16 18:53:23,536] INFO [__main__.main:112] Extracting copy numbers from XML and into CNV with args: {"xml_file": "/tmp/SMP60684.xml", "out_file": "/tmp/output.cnv"} -[2019-05-16 18:53:23,568] INFO [__main__.extract_copy_numbers:64] Extracting copy numbers from xml -[2019-05-16 18:53:23,570] INFO [__main__.write_copy_numbers_to_cnv:90] Saving copy numbers to cnv file